[BioC] NA values
Brooke-Powell, Elizabeth
etbp2 at borcim.wustl.edu
Fri Jul 22 20:09:55 CEST 2005
Just a short question, how does limma and limmaGUI cope with NA values? Or
even does it?
Thanks for your help,
Liz
-----Original Message-----
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Today's Topics:
1. PLIER: two questions (Ariel Chernomoretz)
2. Re: PLIER: two questions (Adaikalavan Ramasamy)
3. Re: PLIER: two questions (Ariel Chernomoretz)
4. NA and quantile normalization (Ravi Murthy)
5. Re: NA and quantile normalization (Ben Bolstad)
6. AffyPLM for Windows (lucia Garc?a)
7. Spikein Data Package Win32 download problem still present
(M.A. Bijl)
----------------------------------------------------------------------
Message: 1
Date: Thu, 21 Jul 2005 11:37:14 -0400
From: Ariel Chernomoretz <ariel.chernomoretz at crchul.ulaval.ca>
Subject: [BioC] PLIER: two questions
To: BioConductor_list <bioconductor at stat.math.ethz.ch>
Message-ID: <200507211137.14168.ariel.chernomoretz at crchul.ulaval.ca>
Content-Type: text/plain; charset="us-ascii"
Hi,
Just a couple of questions about plier
a) With justPlier it is possible to specify as an input vector the replicate
structure of the batch we want to analyze ('replicate' input option).
Can anybody tell me how this information is used by the algorithm? In fact,
can anybody point me to some technical references on how plier works?
b) I found that the 64-bit compiled version of plier presents some
stability
issues (i.e. it crashes). A couple of month ago Adai posted a message
(http://files.protsuggest.org/biocond/html/9034.html) saying that
he solved a similar (I hope) problem.
So, Adai, Crispin, anybody, could you please point me in the right direction
in order to make plier run under my 64-bit Opteron?
Thank you
Ariel./
--
Ariel Chernomoretz, Ph.D.
Centre de recherche du CHUL
2705 Blv Laurier, bloc T-367
Sainte-Foy, Qc
G1V 4G2
(418)-525-4444 ext 46339
------------------------------
Message: 2
Date: Thu, 21 Jul 2005 18:29:55 +0100
From: Adaikalavan Ramasamy <ramasamy at cancer.org.uk>
Subject: Re: [BioC] PLIER: two questions
To: Ariel Chernomoretz <ariel.chernomoretz at crchul.ulaval.ca>
Cc: BioConductor_list <bioconductor at stat.math.ethz.ch>
Message-ID: <1121966995.6531.13.camel at ramasamy.stats>
Content-Type: text/plain
I had the problem when I was submitting it to a cluster. When I actually
ssh-ed into one of the nodes and ran the code interactively, it worked
fine. But then I tried with different array type, I had the segment
fault even with only 3 arrays. So I am not sure if this is a problem
with the cluster queue manager or plier or gcc or something else.
Crispin was quite helpful in suggesting to run it interactively, so I
hope he finds a solution for you.
But I eventually decided not to use PLIER expression measure simply
because no documentation was available explaining it. I prefer knowing
what I am doing than using a black box systems.
I suggest you try RMA or GCRMA which has excellent documentation and has
been shown to be better than MAS 5.0 (which is also well documented).
Regards, Adai
On Thu, 2005-07-21 at 11:37 -0400, Ariel Chernomoretz wrote:
<SNIP>
> b) I found that the 64-bit compiled version of plier presents some
stability
> issues (i.e. it crashes). A couple of month ago Adai posted a message
> (http://files.protsuggest.org/biocond/html/9034.html) saying that
> he solved a similar (I hope) problem.
> So, Adai, Crispin, anybody, could you please point me in the right
direction
> in order to make plier run under my 64-bit Opteron?
------------------------------
Message: 3
Date: Thu, 21 Jul 2005 14:41:12 -0400
From: Ariel Chernomoretz <ariel.chernomoretz at crchul.ulaval.ca>
Subject: Re: [BioC] PLIER: two questions
To: ramasamy at cancer.org.uk
Cc: BioConductor_list <bioconductor at stat.math.ethz.ch>
Message-ID: <200507211441.12853.ariel.chernomoretz at crchul.ulaval.ca>
Content-Type: text/plain; charset="utf-8"
I found some technical info about plier in an oral presentation from E.
Hubbell. You can find it at:
http://mbi.osu.edu/2004/ws1materials/hubbell.ppt
However, I agree with you and think will wait for more documentation in
order
to use plier as a production tool.
Thanks for your time
Ariel./
On July 21, 2005 01:29 pm, Adaikalavan Ramasamy wrote:
> But I eventually decided not to use PLIER expression measure simply
> because no documentation was available explaining it. I prefer knowing
> what I am doing than using a black box syst
--
Ariel Chernomoretz, Ph.D.
Centre de recherche du CHUL
2705 Blv Laurier, bloc T-367
Sainte-Foy, Qc
G1V 4G2
(418)-525-4444 ext 46339
------------------------------
Message: 4
Date: Thu, 21 Jul 2005 13:59:59 -0500
From: "Ravi Murthy" <ravidmurthy at hotmail.com>
Subject: [BioC] NA and quantile normalization
To: bioconductor at stat.math.ethz.ch
Message-ID: <BAY104-F114FF849A830C350C2CE9DA8D60 at phx.gbl>
Content-Type: text/plain; format=flowed
Hi,
I am new to R,
I am doing quantile normalization with a data
consisting of a matix 384 X 124.
While using "normailze.quantiles" I find that it introduces 'NA' into some
of the
cells, where we should expect a numerical value, can someone help me to
overcome this problem ?
The matrix consists of 62 plates in repliccate, and
quantile normailization is done for the data from replicates (colomn 1,2)
using normailze.quantiles function from 'affy' package resulting in data
output as g1
>g1 <- normalize.quantiles(exprs(MSExpr[,1:2]))
etc., uptp g62
This command works well for smaller series of data, but
while using for a larger data matrix, it introduces "NA" in the place where
it is suppose to geneerate data . It doesn't make any
sense because elsewhere in the colomn consisting of similar values it
computes properly.
In addition, if I continue to perform median
normailzation of the quantlies, the function fails to
give any output, execept for those colomns which does
not have any "NA". I cannot get rid of interference of NA in median
normalization by using any of NA related functions.
I am using R in MAC based platform for this analysis.
Please suggest me some way to avoid 'NA' related computation problem.
Ravi
ravidmurthy at hotmail.com
_________________________________________________________________
Dont just search. Find. Check out the new MSN Search!
------------------------------
Message: 5
Date: Thu, 21 Jul 2005 18:12:20 -0700
From: Ben Bolstad <bolstad at stat.berkeley.edu>
Subject: Re: [BioC] NA and quantile normalization
To: Ravi Murthy <ravidmurthy at hotmail.com>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <1121994740.5357.7.camel at localhost.localdomain>
Content-Type: text/plain
If your data initially has NAs then it is quite probable that
normalize.quantiles() would introduce additional NA (or more likely turn
the entire matrix into NA) since it does not make special allowances for
NA values. I think the normalizeQuantiles() function in the limma
package handles NA's more appropriately.
Ben
On Thu, 2005-07-21 at 13:59 -0500, Ravi Murthy wrote:
> Hi,
>
> I am new to R,
> I am doing quantile normalization with a data
> consisting of a matix 384 X 124.
>
> While using "normailze.quantiles" I find that it introduces 'NA' into some
> of the
> cells, where we should expect a numerical value, can someone help me to
> overcome this problem ?
>
> The matrix consists of 62 plates in repliccate, and
> quantile normailization is done for the data from replicates (colomn 1,2)
> using normailze.quantiles function from 'affy' package resulting in data
> output as g1
>
> >g1 <- normalize.quantiles(exprs(MSExpr[,1:2]))
> etc., uptp g62
>
> This command works well for smaller series of data, but
> while using for a larger data matrix, it introduces "NA" in the place
where
> it is suppose to geneerate data . It doesn't make any
> sense because elsewhere in the colomn consisting of similar values it
> computes properly.
>
> In addition, if I continue to perform median
> normailzation of the quantlies, the function fails to
> give any output, execept for those colomns which does
> not have any "NA". I cannot get rid of interference of NA in median
> normalization by using any of NA related functions.
>
> I am using R in MAC based platform for this analysis.
>
> Please suggest me some way to avoid 'NA' related computation problem.
> Ravi
> ravidmurthy at hotmail.com
>
> _________________________________________________________________
> Dont just search. Find. Check out the new MSN Search!
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
------------------------------
Message: 6
Date: Fri, 22 Jul 2005 09:04:36 +0000
From: lucia Garc?a <lucia203 at hotmail.com>
Subject: [BioC] AffyPLM for Windows
To: bioconductor at stat.math.ethz.ch
Message-ID: <BAY103-F523D77A8E41DF6F62DC188CC90 at phx.gbl>
Content-Type: text/plain; charset=iso-8859-1; format=flowed
Hi,
I`m interesting in update AffyPLM to version 1.4.2, but it's only to linux
version, but to windows package is 1.3.3. When it will be available the
version 1.4.2 for windows? I need this version to fix an error in data of
Yeast.
This erro will be fixed in affylmGUI?
Thanks
_________________________________________________________________
Descarga gratis la Barra de Herramientas de MSN
------------------------------
Message: 7
Date: Fri, 22 Jul 2005 11:03:15 +0200
From: "M.A. Bijl" <m.a.bijl at erasmusmc.nl>
Subject: [BioC] Spikein Data Package Win32 download problem still
present
To: bioconductor at stat.math.ethz.ch
Message-ID: <42E0B653.8080005 at erasmusmc.nl>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi,
There is an exact same mailinglist message (dated Mon Jun 20 2005). It's
said the problem is fixed, but I guess it isn't.
I still can't seem to download the Win32 SpikeIn package from the
Experiment Data Packages section (both 1.6 stable and 1.7 devel) :
******start error message******
Access forbidden!
You don't have permission to access the requested object. It is either
read-protected or not readable by the server.
If you think this is a server error, please contact the webmaster
<mailto:undefined at cobra.fhcrc.org>.
Error 403
www.bioconductor.org <http://www.bioconductor.org/>
Fri Jul 22 01:43:08 2005
Apache/2.0.49 (Linux/SuSE)
******end error message******
The unix source, again, is fine.
If some one could please look into this it would be highly appreciated.
Thanks for your attention!
Maarten
--
B.ICT M.A. Bijl
Erasmus MC
Dept. of Bioinformatics, Rm. 15.32a/b
Dr. Molewaterplein 50
3000 DR Rotterdam
The Netherlands
TEL: +31 10 40 89381
FAX: +31 10 40 88161
------------------------------
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