[BioC] Cluster analysis distance measuer
Auer Michael
michael.auer at meduniwien.ac.at
Wed Nov 10 18:10:35 CET 2004
I would like to know wheter there exists the possibility to cluster genes
non-hierachically, but with the correlation as distance measure? K-means,
clara, pam, etc, only seem to work with euclidean metrics. I aks the
question because the number of genes is often too big to apply
hierarchical clustering, and the distance measure has a strong influence
on the way genes are clusterd.
Thanks
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> Today's Topics:
>
> 1. error following cluster example (kfbargad at lg.ehu.es)
> 2. RE: error following cluster example (Claire Wilson)
> 3. Re: error following cluster example (Robert Gentleman)
> 4. Re: AnnBuilder bug // R-2.0.0 // getList4GO (John Zhang)
> 5. comparing different experiments (Julia Engelmann)
> 6. Problems with heatmap on genes... (Giulio Di Giovanni)
> 7. help with limma contrast matrix (Kimpel, Mark W)
> 8. RE: Problems with heatmap on genes... (michael watson (IAH-C))
> 9. Re: Problems with heatmap on genes... (jeffrey rasmussen)
> 10. Re: comparing different experiments (Fangxin Hong)
> 11. affy segmentation fault (Sucheta Tripathy)
> 12. Re: affy segmentation fault (Adaikalavan Ramasamy)
> 13. Re: affy segmentation fault (Ben Bolstad)
> 14. Re: affy segmentation fault (Sucheta Tripathy)
> 15. Re: affy segmentation fault (Adaikalavan Ramasamy)
> 16. RE: Problems with heatmap on genes... (Johan Lindberg)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 9 Nov 2004 12:59:41 +0100 (CET)
> From: kfbargad at lg.ehu.es
> Subject: [BioC] error following cluster example
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <9456297971kfbargad at lg.ehu.es>
> Content-Type: text/plain; charset="ISO-8859-1"
>
> Dear Users,
>
> I am following the example on Lab 5: Cluster analysis (June 2003) with
> my own data.
>
> I have filtered my expression set as shown on the example and I get
> the following
>
>> sub <- genefilter(X,ffun)
>> sum(sub)
> [1] 1124
>
> I save this subset of genes and then log transform it. But when I type
> the next command I get the following error:
>> X <- X[sub,]
>> X <- log2(X)
>> RawDataSub <- Raw.Data[,sub]
> Error in Raw.Data[, sub] : (subscript) logical subscript too long
>
> Why do I get this error??
> Also, if I have stored the subset expression data as X, why is Raw.Data
> [,sub] using [,sub] again? I don´t really understand this step, if
> anyone could explain its purpose.
>
> I´m running R 1.9.1 on an XP computer
>
> Thanks a lot for your help
>
> David
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 9 Nov 2004 12:29:19 -0000
> From: "Claire Wilson" <ClaireWilson at PICR.man.ac.uk>
> Subject: RE: [BioC] error following cluster example
> To: <kfbargad at lg.ehu.es>, <bioconductor at stat.math.ethz.ch>
> Message-ID:
> <BAA35444B19AD940997ED02A6996AAE001DE15E7 at sanmail.picr.man.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
>
>> Dear Users,
>>
>> I am following the example on Lab 5: Cluster analysis (June
>> 2003) with
>> my own data.
>>
>> I have filtered my expression set as shown on the example and I get
>> the following
>>
>> > sub <- genefilter(X,ffun)
>> > sum(sub)
>> [1] 1124
>>
>> I save this subset of genes and then log transform it. But
>> when I type
>> the next command I get the following error:
>> > X <- X[sub,]
>> > X <- log2(X)
>> > RawDataSub <- Raw.Data[,sub]
>> Error in Raw.Data[, sub] : (subscript) logical subscript too long
>
> it looks like you are tyring to select columns not rows,
> RawDataSub <- Raw.Data[,sub] #subsets on columns
> try:
> RawDataSub <- Raw.Data[sub,] #subset on rows
>
> hth
>
> claire
>
> --------------------------------------------------------
>
>
> This email is confidential and intended solely for the use o...{{dropped}}
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 9 Nov 2004 08:07:59 -0500
> From: Robert Gentleman <rgentlem at jimmy.harvard.edu>
> Subject: Re: [BioC] error following cluster example
> To: kfbargad at lg.ehu.es
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <20041109080759.E29793 at jimmy.harvard.edu>
> Content-Type: text/plain; charset=iso-8859-1
>
> On Tue, Nov 09, 2004 at 12:59:41PM +0100, kfbargad at lg.ehu.es wrote:
>> Dear Users,
>>
>> I am following the example on Lab 5: Cluster analysis (June 2003) with
>> my own data.
>>
>> I have filtered my expression set as shown on the example and I get
>> the following
>>
>> > sub <- genefilter(X,ffun)
>> > sum(sub)
>> [1] 1124
>>
>> I save this subset of genes and then log transform it. But when I type
>> the next command I get the following error:
>> > X <- X[sub,]
>> > X <- log2(X)
>> > RawDataSub <- Raw.Data[,sub]
>> Error in Raw.Data[, sub] : (subscript) logical subscript too long
>>
>> Why do I get this error??
>
> Perhaps because the dimensions of X and of Raw.Data are not the
> same? If you are not familiar with R you should spend some time with
> introductory material to learn about the language as that knowledge
> is essential for debugging.
>
>> Also, if I have stored the subset expression data as X, why is Raw.Data
>> [,sub] using [,sub] again? I don´t really understand this step, if
>> anyone could explain its purpose.
>>
>
> Because X and Raw.Data are not the same object. R basically has pass
> by value semantics and so (almost) everything is a copy.
>
>> I´m running R 1.9.1 on an XP computer
>>
>> Thanks a lot for your help
>>
>> David
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> --
> +---------------------------------------------------------------------------+
> | Robert Gentleman phone : (617) 632-5250
> |
> | Associate Professor fax: (617) 632-2444
> |
> | Department of Biostatistics office: M1B20
> |
> | Harvard School of Public Health email: rgentlem at jimmy.harvard.edu
> |
> +---------------------------------------------------------------------------+
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 9 Nov 2004 08:32:08 -0500 (EST)
> From: John Zhang <jzhang at jimmy.harvard.edu>
> Subject: Re: [BioC] AnnBuilder bug // R-2.0.0 // getList4GO
> To: hathanassiou at automatedcell.com
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <200411091332.IAA26906 at blaise.dfci.harvard.edu>
> Content-Type: TEXT/plain; charset=us-ascii
>
> Thanks. I will have a look at the code and fix the problem.
>
>>From: "Harry Athanassiou" <hathanassiou at automatedcell.com>
>>To: <bioconductor at stat.math.ethz.ch>
>>Date: Tue, 9 Nov 2004 01:22:42 -0500
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>>Subject: [BioC] AnnBuilder bug // R-2.0.0 // getList4GO
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>>
>>I'm trying to use AnnBuilder to make some custom annotation files for a
>>non-standard microarray chip. In running the tests with R-2.0.0, I run
>>acroos a problem in the function getList4GO. I'm not sure if this issue
>> is
>>due to R-2.0.0 or not.
>>
>>Here's the issue:
>>when the sub-function procOne is called by sapply, the names(goids) is
>> NULL.
>>Thus when procOne calls :
>> apply(temp, 1, vect2List, vectNames = c("GOID", "Evidence",
>> "Ontology"))
>>the number of list-elements to be named is mismatched.
>>
>>I do not know how to make sapply pass the names() of its first argument
>> to
>>the FUN() it calls, so I modified procOne->procOne.new to drop the column
>>"Evidence".
>>And add this column with a trick afterwards.
>>
>>I'm sure this is not the best solution, just worked for me
>>
>>>>>
>>getList4GO <- function (goNCat, goNEvi)
>>{
>> procOne <- function(goids) {
>> if (is.null(goids) || is.na(goids)) {
>> return(NA)
>> }
>> else {
>> temp <- cbind(goids, names(goids), goNCat[goids])
>> rownames(temp) <- goids
>> return(apply(temp, 1, vect2List, vectNames = c("GOID",
>>"Evidence", "Ontology")))
>> }
>> }
>>
>> # the names(goids) do not get propagated through the sapply() in
>>R-2.0.0!
>> # remove the column evidence
>> procOne.new <- function(goids) {
>> if (is.null(goids) || is.na(goids)) {
>> return(NA)
>> }
>> else {
>> temp <- cbind(goids, goNCat[goids])
>> rownames(temp) <- goids
>> return(apply(temp, 1, vect2List, vectNames = c("GOID",
>>"Ontology")))
>> }
>> }
>>
>> temp <- sapply(goNEvi, procOne.new)
>> names(temp) <- 1:length(temp)
>>
>> # add the evidence list-element
>> # do not know a better way will do a loop on an index to acc two
>> arrays
>>at the same time
>> for (r in 1:length(goNEvi)) {
>> if (!is.na(temp[r])) {
>> temp[[r]] <- c(temp[[r]], "Evidence"=names(goNEvi)[r])
>> }
>> }
>>
>> return(temp)
>>}
>>>>>
>>
>>Harry Athanassiou
>>BioInformatics manager
>>Automated Cell, Inc
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> Jianhua Zhang
> Department of Biostatistics
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 09 Nov 2004 16:30:53 +0100
> From: Julia Engelmann <julia.engelmann at biozentrum.uni-wuerzburg.de>
> Subject: [BioC] comparing different experiments
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <4190E2AD.1060501 at biozentrum.uni-wuerzburg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi list,
>
> I wonder if I can compare Affymetrix arrays of the same type (ATH1)
> which were made in different laboratories and with different tissue
> types and different references. I have: "tissue1 treated", "tissue1
> untreated" from one lab and "tissue2 treated", "tissue2 untreated" from
> the other lab.
> The references (untreated) are different because of the different
> tissue types. I am interested in the difference between tissue1 treated
> and tissue2 treated, so I thought I could use limma to make a contrast:
> (tissue1_treated-tissue1_untreated)-(tissue2_treated-tissue2_untreated).
> I am not sure if this is valid, though? For example, I do not account
> for the different labs that way.
> Maybe it is just possible to analyse each experiment by itself and
> compare the results at a latter stage, say compare lists of
> differentially expressed genes?
>
> Any advice, comments or hints are highly appreciated,
>
> Julia
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 09 Nov 2004 15:37:56 +0000
> From: "Giulio Di Giovanni" <perimessaggini at hotmail.com>
> Subject: [BioC] Problems with heatmap on genes...
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <BAY10-F38BmhwRHiU340003395b at hotmail.com>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed
>
>
> Hi,
>
> I'm trying to have a clear figure of gene clusters using heatmaps, but
> with
> more than 100-200 genes it's not possible to do it, with default options
> (and I would like to do that with 1500 genes or so...). Gene names (and
> branchs too) collapse together...
>
> I tried, setting new device dimensions (jpeg() or png() height and width),
> and modifying par() options (fin, etc..), to have long cluster figures (to
> be clear, dChip style). Well, it works for others high-level graphical
> functions, but it doesn't work for heatmaps(). I always obtain big
> figures,
> but with exactely the same squared heatmap inside.
>
> I spent long time on the documentation and searching the web, and when I
> found something, it was always some heatmaps for 50-100 genes at max
>
> I trust that someone working on gene clustering is confidential on this,
> and I will appreciate a lot any suggestion... I almost became crazy on
> that
> !!!
>
> Thanks in advance,
>
> Giulio
>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 9 Nov 2004 11:54:55 -0500
> From: "Kimpel, Mark W" <mkimpel at iupui.edu>
> Subject: [BioC] help with limma contrast matrix
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID:
> <2E6C5260C7C387449A96DF46EE76313C017D8985 at iu-mssg-mbx02.exchange.iu.edu>
>
> Content-Type: text/plain; charset="us-ascii"
>
> I would appreciate advice on how to construct a contrast matrix for a
> 5X2 ANOVA design. Briefly, I have a genomic experiment to analyze that
> compares 5 brain regions in 2 strains of rats. We are interested in
> discovering overall differences between strains (collapsing all brain
> regions together) but also discovering differences that may only be
> expressed in one brain region.
>
> I have attempted to construct the appropriate matrix with the code
> listed below, but it does not work. I seem to get differences between
> strains, but all the brain region contrasts give exactly the same
> results, so I know something isn't correct.
>
> contrast <-makeContrasts(
>
> (
> (NPAccumbens + NPAmygdala + NPHippocampus + NPPrefrontal_Cortex
> + NPStriatum) - #all regions of strain "NP"
>
> (PAccumbens + PAmygdala + PHippocampus + PPrefrontal_Cortex +
> PStriatum) #all regions of strain "P"
>
> ),
>
> (NPAccumbens - PAccumbens),
> #accumbens region of both strains
>
> (NPAmygdala - PAmygdala),
> #amygdala region of both strains
>
> (NPHippocampus - PHippocampus),
> #hippocampus region of both strains
>
> (NPPrefrontal_Cortex - PPrefrontal_Cortex),
> #Prefrontal_Cortex region of both strains
>
> (NPStriatum - PStriatum),
> #striatum region of both strains
>
> levels=design)
>
>
> Thanks!
>
> Mark
>
> Mark W. Kimpel MD
>
>
>
> (317) 490-5129 Home, Work, & Mobile
>
> (317) 278-4104 FAX
>
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 9 Nov 2004 16:54:09 -0000
> From: "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk>
> Subject: RE: [BioC] Problems with heatmap on genes...
> To: "Giulio Di Giovanni" <perimessaggini at hotmail.com>,
> <bioconductor at stat.math.ethz.ch>
> Message-ID:
> <8975119BCD0AC5419D61A9CF1A923E950121B868 at iahce2knas1.iah.bbsrc.reserved>
>
> Content-Type: text/plain; charset="Windows-1252"
>
> Hi
>
> There's a function called heatmap.2 in the gregmisc library that will
> resize properly when you send it to a long png() or jpg().
>
> It's similar to, but not the same as, heatmap() so read the docs!
>
> Mick
>
>
> -----Original Message-----
> From: Giulio Di Giovanni [mailto:perimessaggini at hotmail.com]
> Sent: Tue 11/9/2004 3:37 PM
> To: bioconductor at stat.math.ethz.ch
> Cc:
> Subject: [BioC] Problems with heatmap on genes...
>
> Hi,
>
> I'm trying to have a clear figure of gene clusters using heatmaps, but
> with
> more than 100-200 genes it's not possible to do it, with default options
> (and I would like to do that with 1500 genes or so...). Gene names (and
> branchs too) collapse together...
>
> I tried, setting new device dimensions (jpeg() or png() height and width),
> and modifying par() options (fin, etc..), to have long cluster figures (to
> be clear, dChip style). Well, it works for others high-level graphical
> functions, but it doesn't work for heatmaps(). I always obtain big
> figures,
> but with exactely the same squared heatmap inside.
>
> I spent long time on the documentation and searching the web, and when I
> found something, it was always some heatmaps for 50-100 genes at max
>
> I trust that someone working on gene clustering is confidential on this,
> and I will appreciate a lot any suggestion... I almost became crazy on
> that
> !!!
>
> Thanks in advance,
>
> Giulio
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
>
> ------------------------------
>
> Message: 9
> Date: Tue, 9 Nov 2004 09:14:23 -0800 (PST)
> From: jeffrey rasmussen <rasmuss at u.washington.edu>
> Subject: Re: [BioC] Problems with heatmap on genes...
> To: Giulio Di Giovanni <perimessaggini at hotmail.com>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID:
> <Pine.A41.4.61b.0411090909320.309756 at homer11.u.washington.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Hi Giulio,
>
> If you have access to Adobe Illustrator, you could write your heatmap to a
> postscript file using postscript() and then open and edit the file in
> Illustrator. I've found that in many cases this is much easier than
> wrangling with the plotting parameters in R, in particular when it comes
> to fonts. Otherwise, trying to display > 50 genes on a heatmap becomes
> prohibitively difficult.
>
> Best,
> Jeff.
>
> On Tue, 9 Nov 2004, Giulio Di Giovanni wrote:
>
>>
>> Hi,
>>
>> I'm trying to have a clear figure of gene clusters using heatmaps, but
>> with
>> more than 100-200 genes it's not possible to do it, with default options
>> (and
>> I would like to do that with 1500 genes or so...). Gene names (and
>> branchs
>> too) collapse together...
>>
>> I tried, setting new device dimensions (jpeg() or png() height and
>> width),
>> and modifying par() options (fin, etc..), to have long cluster figures
>> (to be
>> clear, dChip style). Well, it works for others high-level graphical
>> functions, but it doesn't work for heatmaps(). I always obtain big
>> figures,
>> but with exactely the same squared heatmap inside.
>>
>> I spent long time on the documentation and searching the web, and when I
>> found something, it was always some heatmaps for 50-100 genes at max
>>
>> I trust that someone working on gene clustering is confidential on this,
>> and I will appreciate a lot any suggestion... I almost became crazy on
>> that
>> !!!
>>
>> Thanks in advance,
>>
>> Giulio
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Tue, 9 Nov 2004 13:26:19 -0800 (PST)
> From: "Fangxin Hong" <fhong at salk.edu>
> Subject: Re: [BioC] comparing different experiments
> To: "Julia Engelmann" <julia.engelmann at biozentrum.uni-wuerzburg.de>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <1630.10.10.200.250.1100035579.squirrel at 10.10.200.250>
> Content-Type: text/plain;charset=iso-8859-1
>
>
>> I wonder if I can compare Affymetrix arrays of the same type (ATH1)
>> which were made in different laboratories and with different tissue
>> types and different references. I have: "tissue1 treated", "tissue1
>> untreated" from one lab and "tissue2 treated", "tissue2 untreated" from
>> the other lab.
>> The references (untreated) are different because of the different
>> tissue types. I am interested in the difference between tissue1 treated
>> and tissue2 treated, so I thought I could use limma to make a contrast:
>> (tissue1_treated-tissue1_untreated)-(tissue2_treated-tissue2_untreated).
>> I am not sure if this is valid, though? For example, I do not account
>> for the different labs that way.
>> Maybe it is just possible to analyse each experiment by itself and
>> compare the results at a latter stage, say compare lists of
>> differentially expressed genes?
> Based on what I observed when study data generated at different lab, lab
> effect can't not be completely removed by normalization step. If you do
> have some replicates or several data sets from each lab, and you want to
> combine data together, I would suggest you to inlcude a fixed effect for
> lab factor.
> Hopefully this will help.
>
> Fangxin
>
>
> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>
>
>
> --
> Fangxin Hong, Ph.D.
> Plant Biology Laboratory
> The Salk Institute
> 10010 N. Torrey Pines Rd.
> La Jolla, CA 92037
> E-mail: fhong at salk.edu
>
>
>
> ------------------------------
>
> Message: 11
> Date: Tue, 9 Nov 2004 16:46:03 -0500 (EST)
> From: "Sucheta Tripathy" <sutripa at vbi.vt.edu>
> Subject: [BioC] affy segmentation fault
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <1815.199.3.136.4.1100036763.squirrel at webmail.vbi.vt.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
>
> I know we have been cluttering this mailing list with this question over
> and again. The reason I want to ask again is after seeing the segmentation
> fault error, I found it says 340000 KB to be the size it needs.
>
> What puzzles me is our memory is way beyond that(almost 5 GB with 10 GB
> swap memory).
>
> After trying all the remedies, it still fails. Can anyone suggest if in
> the source where the exact memory allocation takes place, how much is
> fixed to be the size. Can we not increase it? Or to begin with which
> version of affy package has a fix for it.
>
> Thanks in advance.
>
> Sucheta
>
> --
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax: (540) 231-2606
>
>
>
> ------------------------------
>
> Message: 12
> Date: Tue, 09 Nov 2004 22:46:04 +0000
> From: Adaikalavan Ramasamy <ramasamy at cancer.org.uk>
> Subject: Re: [BioC] affy segmentation fault
> To: Sucheta Tripathy <sutripa at vbi.vt.edu>
> Cc: BioConductor mailing list <bioconductor at stat.math.ethz.ch>
> Message-ID: <1100040364.3326.10.camel at localhost.localdomain>
> Content-Type: text/plain
>
> I just checked the mailing archives. You sent 2 mails in Novembers
> (excluding this) and 2 in October but none of them talk about
> segmentation fault error. Perhaps you can explain who "we" are or better
> yet state the problem or link to past mail (perhaps from
> https://stat.ethz.ch/pipermail/bioconductor/).
>
> Start from a clean R session and see if you can repeat the problem.
> Next, reduce the number of arrays till you find out how many arrays your
> machine can handle. Try just.rma or just.gcrma. Also search the mailing
> archives. These are all guesses.
>
> Note that although 5 GB is available to a machine, there might be a
> limit to how much each process/user can have access to. Speak to your
> system administrator about any such limitation.
>
> Regards, Adai
>
>
>
> On Tue, 2004-11-09 at 21:46, Sucheta Tripathy wrote:
>> I know we have been cluttering this mailing list with this question over
>> and again. The reason I want to ask again is after seeing the
>> segmentation
>> fault error, I found it says 340000 KB to be the size it needs.
>>
>> What puzzles me is our memory is way beyond that(almost 5 GB with 10 GB
>> swap memory).
>>
>> After trying all the remedies, it still fails. Can anyone suggest if in
>> the source where the exact memory allocation takes place, how much is
>> fixed to be the size. Can we not increase it? Or to begin with which
>> version of affy package has a fix for it.
>>
>> Thanks in advance.
>>
>> Sucheta
>
>
>
> ------------------------------
>
> Message: 13
> Date: Tue, 09 Nov 2004 14:49:05 -0800
> From: Ben Bolstad <bolstad at stat.berkeley.edu>
> Subject: Re: [BioC] affy segmentation fault
> To: Sucheta Tripathy <sutripa at vbi.vt.edu>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <1100040545.2398.70.camel at bmbbox.dyndns.org>
> Content-Type: text/plain
>
> Please wait for the next version of the affy package 1.6.0 which should
> appear on the web in a few days. It has the requisite fix to deal with
> your soybean arrays.
>
> Ben
>
>
>
> On Tue, 2004-11-09 at 13:46, Sucheta Tripathy wrote:
>> I know we have been cluttering this mailing list with this question over
>> and again. The reason I want to ask again is after seeing the
>> segmentation
>> fault error, I found it says 340000 KB to be the size it needs.
>>
>> What puzzles me is our memory is way beyond that(almost 5 GB with 10 GB
>> swap memory).
>>
>> After trying all the remedies, it still fails. Can anyone suggest if in
>> the source where the exact memory allocation takes place, how much is
>> fixed to be the size. Can we not increase it? Or to begin with which
>> version of affy package has a fix for it.
>>
>> Thanks in advance.
>>
>> Sucheta
> --
> Ben Bolstad <bolstad at stat.berkeley.edu>
> http://www.stat.berkeley.edu/~bolstad
>
>
>
> ------------------------------
>
> Message: 14
> Date: Tue, 09 Nov 2004 18:51:17 -0500
> From: Sucheta Tripathy <sutripa at vbi.vt.edu>
> Subject: Re: [BioC] affy segmentation fault
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <5.1.0.14.0.20041109183629.01f966c8 at mail.vbi.vt.edu>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
>
> At 04:59 PM 11/9/2004 -0500, Robert Gentleman wrote:
>>On Tue, Nov 09, 2004 at 04:46:03PM -0500, Sucheta Tripathy wrote:
>> >
>> > I know we have been cluttering this mailing list with this question
>> over
>> > and again. The reason I want to ask again is after seeing the
>> segmentation
>> > fault error, I found it says 340000 KB to be the size it needs.
>> >
>> > What puzzles me is our memory is way beyond that(almost 5 GB with 10
>> GB
>> > swap memory).
>>
>> And as I have said very many times already, it likely has nothing to
>> do with that, but rather that you have a corrupted installation. You
>> almost surely need to recompile R with the correct set of compiler
>> flags for your system and to reinstall the the appropriate
>> packages. I am not sure how I can say this more explicitly, but the
>> problem does not seem to be affy, it seems to be your installation.
>
> I guess at this point if any body else who has done installation and
> compilation with any other flag, shares the flags they have used, I will
> really appreciate that. After digging through the installation
> instruction,
> I don't find anything other than
>
> $ ./configure
> $ make
>
> with may be a option to prefix path.(where R binaries and libraries should
> go).
>
> Probably I need help from someone who can point where to find a more
> detailed installation help. I have been also looking at file config.site,
> and most of the default options look fine to me.
>
> If it is just the case of R being corrupted,is no big deal provided we
> know
> what flags we are using to compile next.
>
> -Sucheta
>
>> Robert
>>
>>
>> >
>> > After trying all the remedies, it still fails. Can anyone suggest if
>> in
>> > the source where the exact memory allocation takes place, how much is
>> > fixed to be the size. Can we not increase it? Or to begin with which
>> > version of affy package has a fix for it.
>> >
>> > Thanks in advance.
>> >
>> > Sucheta
>> >
>> > --
>> > Sucheta Tripathy
>> > Virginia Bioinformatics Institute Phase-I
>> > Washington street.
>> > Virginia Tech.
>> > Blacksburg,VA 24061-0447
>> > phone:(540)231-8138
>> > Fax: (540) 231-2606
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>--
>>+---------------------------------------------------------------------------+
>>| Robert Gentleman phone : (617) 632-5250
>> |
>>| Associate Professor fax: (617) 632-2444
>> |
>>| Department of Biostatistics office: M1B20
>> |
>>| Harvard School of Public Health email: rgentlem at jimmy.harvard.edu
>> |
>>+---------------------------------------------------------------------------+
>
>
>
> ------------------------------
>
> Message: 15
> Date: Wed, 10 Nov 2004 08:16:32 +0000
> From: Adaikalavan Ramasamy <ramasamy at cancer.org.uk>
> Subject: Re: [BioC] affy segmentation fault
> To: Sucheta Tripathy <sutripa at vbi.vt.edu>
> Cc: BioConductor mailing list <bioconductor at stat.math.ethz.ch>
> Message-ID: <1100074592.7513.41.camel at localhost.localdomain>
> Content-Type: text/plain
>
> A normal installation procedure for me would be something like :
>
> make clean # or make distclean if you tried configuring before
> ./configure --prefix=/home/adai/R
> make
> make check
> make install
>
> There are variants of versions of 'make check' such as 'make check-all'
> which are more comprehensive testing (see page 3 of R-admin).
>
> I do not know comprehend the flags and various options. If there is an
> error or problem, I usually get my system administrator involved and
> failing that I would try R-help mailing which is the more appropriate
> place.
>
> And when you email R-help, please mention some vital information such as
> your operating system (and kernel), gcc version, R version. Have you
> tried checking R-help or BioC mailing archives ?
>
> BTW, does Ben Bolstad's reply about affy 1.6.0. answer your question ?
>
>
>
> On Tue, 2004-11-09 at 23:51, Sucheta Tripathy wrote:
>> At 04:59 PM 11/9/2004 -0500, Robert Gentleman wrote:
>> >On Tue, Nov 09, 2004 at 04:46:03PM -0500, Sucheta Tripathy wrote:
>> > >
>> > > I know we have been cluttering this mailing list with this question
>> over
>> > > and again. The reason I want to ask again is after seeing the
>> segmentation
>> > > fault error, I found it says 340000 KB to be the size it needs.
>> > >
>> > > What puzzles me is our memory is way beyond that(almost 5 GB with 10
>> GB
>> > > swap memory).
>> >
>> > And as I have said very many times already, it likely has nothing to
>> > do with that, but rather that you have a corrupted installation. You
>> > almost surely need to recompile R with the correct set of compiler
>> > flags for your system and to reinstall the the appropriate
>> > packages. I am not sure how I can say this more explicitly, but the
>> > problem does not seem to be affy, it seems to be your installation.
>>
>> I guess at this point if any body else who has done installation and
>> compilation with any other flag, shares the flags they have used, I will
>> really appreciate that. After digging through the installation
>> instruction,
>> I don't find anything other than
>>
>> $ ./configure
>> $ make
>>
>> with may be a option to prefix path.(where R binaries and libraries
>> should go).
>>
>> Probably I need help from someone who can point where to find a more
>> detailed installation help. I have been also looking at file
>> config.site,
>> and most of the default options look fine to me.
>>
>> If it is just the case of R being corrupted,is no big deal provided we
>> know
>> what flags we are using to compile next.
>>
>> -Sucheta
>>
>> > Robert
>> >
>> >
>> > >
>> > > After trying all the remedies, it still fails. Can anyone suggest if
>> in
>> > > the source where the exact memory allocation takes place, how much
>> is
>> > > fixed to be the size. Can we not increase it? Or to begin with which
>> > > version of affy package has a fix for it.
>> > >
>> > > Thanks in advance.
>> > >
>> > > Sucheta
>> > >
>> > > --
>> > > Sucheta Tripathy
>> > > Virginia Bioinformatics Institute Phase-I
>> > > Washington street.
>> > > Virginia Tech.
>> > > Blacksburg,VA 24061-0447
>> > > phone:(540)231-8138
>> > > Fax: (540) 231-2606
>> > >
>> > > _______________________________________________
>> > > Bioconductor mailing list
>> > > Bioconductor at stat.math.ethz.ch
>> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >
>> >--
>> >+---------------------------------------------------------------------------+
>> >| Robert Gentleman phone : (617) 632-5250
>> |
>> >| Associate Professor fax: (617) 632-2444
>> |
>> >| Department of Biostatistics office: M1B20
>> |
>> >| Harvard School of Public Health email: rgentlem at jimmy.harvard.edu
>> |
>> >+---------------------------------------------------------------------------+
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>
>
>
> ------------------------------
>
> Message: 16
> Date: Wed, 10 Nov 2004 09:43:43 +0100
> From: "Johan Lindberg" <johanl at biotech.kth.se>
> Subject: RE: [BioC] Problems with heatmap on genes...
> To: "'Giulio Di Giovanni'" <perimessaggini at hotmail.com>,
> <bioconductor at stat.math.ethz.ch>
> Message-ID: <000b01c4c701$62f059b0$27230a0a at biochem.kth.se>
> Content-Type: text/plain; charset="US-ASCII"
>
> Hi Giulio. Heatmap is as you say a great tool if you have a small number
> of genes but NOT if you have a lot of genes. I was dealing with the same
> thing as you are doing now some 6 month ago and I found no good solution
> using Heatmap. Therefore we use the freeware (note freeware) MeV from
> TIGR at our department to do hierarchical clustering and similar things.
>
> http://www.tigr.org/software/tm4/mev.html
>
> What we have done is to write a script (exportMEV) that takes an
> MA-object (package Aroma in R) and export that object to MeV format and
> use it when doing clustering.
> http://www.biotech.kth.se/molbio/microarray/pages/kthpackagetransfer.htm
> l
>
> Best regards
>
> // Johan Lindberg
>
>
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Giulio Di
> Giovanni
> Sent: Tuesday, November 09, 2004 4:38 PM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Problems with heatmap on genes...
>
>
> Hi,
>
> I'm trying to have a clear figure of gene clusters using heatmaps, but
> with
> more than 100-200 genes it's not possible to do it, with default options
>
> (and I would like to do that with 1500 genes or so...). Gene names (and
> branchs too) collapse together...
>
> I tried, setting new device dimensions (jpeg() or png() height and
> width),
> and modifying par() options (fin, etc..), to have long cluster figures
> (to
> be clear, dChip style). Well, it works for others high-level graphical
> functions, but it doesn't work for heatmaps(). I always obtain big
> figures,
> but with exactely the same squared heatmap inside.
>
> I spent long time on the documentation and searching the web, and when I
>
> found something, it was always some heatmaps for 50-100 genes at max
>
> I trust that someone working on gene clustering is confidential on this,
> and I will appreciate a lot any suggestion... I almost became crazy on
> that
> !!!
>
> Thanks in advance,
>
> Giulio
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
>
> ------------------------------
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
> End of Bioconductor Digest, Vol 21, Issue 10
> ********************************************
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