[BioC] Ecoli antisense library
James W. MacDonald
jmacdon at med.umich.edu
Mon Mar 22 19:27:34 CET 2010
Bala,
Again. Please don't take things off list. In other words, you shouldn't
be responding to me alone. Instead, respond to all so our conversation
goes back to the list. The whole purpose of this list is to be a
repository of information that people can use to answer questions
themselves. If you keep taking things off list, then this cannot be of
any help to people in the future.
Balasubramanian Ganesan wrote:
> Hi Jim
> It is GSE 7398.
> Here's the link to it below.
> BALA
>
> http://www.ncbi.nlm.nih.gov/gds/?term=GSE7398
The problem with these chips is that they are a mixture of EcoliASv2 and
Ecoliantisense chips, so you will have to process them separately.
First, let's look at what the chips are:
> lst2 <- lapply(lst, affyio:::read.celfile.header)
> names(lst2) <- list.celfiles()
> sapply(lst2, function(x) x[1])
$GSM177549.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177550.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177551.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177552.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177553.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177554.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177555.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177556.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177557.CEL.cdfName
[1] "Ecoli_ASv2"
$GSM177558.CEL.cdfName
[1] "Ecoli_ASv2"
$GSM177559.CEL.cdfName
[1] "Ecoli_ASv2"
$GSM177560.CEL.cdfName
[1] "Ecoli_ASv2"
$GSM177561.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177562.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177563.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177564.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177565.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177566.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177567.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177568.CEL.cdfName
[1] "Ecoli_antisense"
$GSM177569.CEL.cdfName
[1] "Ecoli_ASv2"
$GSM177570.CEL.cdfName
[1] "Ecoli_ASv2"
$GSM177571.CEL.cdfName
[1] "Ecoli_ASv2"
$GSM177572.CEL.cdfName
[1] "Ecoli_ASv2"
Now make an index to separate the two chip types
> ind1 <- which(sapply(lst2, function(x) x[1]) == "Ecoli_ASv2")
> ind1
GSM177557.CEL.cdfName GSM177558.CEL.cdfName GSM177559.CEL.cdfName
9 10 11
GSM177560.CEL.cdfName GSM177569.CEL.cdfName GSM177570.CEL.cdfName
12 21 22
GSM177571.CEL.cdfName GSM177572.CEL.cdfName
23 24
And process each type separately:
> eset1 <- justRMA(filenames=list.celfiles()[ind1],
cdfname="ecoliantisensecdf")
> eset2 <- justRMA(filenames=list.celfiles()[-ind1])
Best,
Jim
>
>
> On Mon, Mar 22, 2010 at 9:47 AM, James W. MacDonald
> <jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>> wrote:
>
> Hi Bala,
>
> What GEO dataset are you using?
>
> Jim
>
>
>
> Balasubramanian Ganesan wrote:
>
> Dear Jim
> Sorry I didn't mean to hold back but do not quite understand
> what to say - please see below.
> I tried two different approaches - 1) install ecoliasv2cdf
> available as a Bioconductor package and 2) rmove the
> Bioconductor package and install the cdf library I downloaded
> from Affy's website using "make.cdf.package" and "R CMD INSTALL".
> When I type the following commands after restarting the R GUI:
> > library(affy)
> > setwd("<path-to-cel-files>")
> > eset <- justRMA(cdfname = "ecoliasv2cdf")
>
> At this point R crashes. I tried waiting for up to 10 min before
> force-quitting R.
> I also tried the following:
> > library(affy)
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> > setwd("<path-2-cel-files>")
> > data<-ReadAffy(cdfname="ecoliasv2cdf")
> Error in read.affybatch(filenames = l$filenames, phenoData =
> l$phenoData, : Cel file /<path>/xyz.CEL does not seem to be
> of Ecoli_antisense type
> >
> I am doing this in R 2.9.0 installed on an Apple Intel Core Duo
> machine running OS X Leopard 10.5.8.
> If you need more information pl. do let me know.
> Thank you for trying to help me.
> BALA
>
> On Wed, Mar 17, 2010 at 3:48 PM, James MacDonald
> <jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>
> <mailto:jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>>>
> wrote:
>
> Please don't take things off-list. The list archives are
> considered
> a resource for others to search for answers.
>
>
> Balasubramanian Ganesan wrote:
>
> Hi Jim
> This doesn't seem to help.
> Any other suggestions?
>
>
> You're going to have to give more input than that. What happens?
> What exactly did you do? Did you try installing the
> ecoliasv2cdf first?
>
> Best,
>
> Jim
>
>
> Thanks
> BALA
>
>
> On Wed, Mar 17, 2010 at 10:06 AM, James W. MacDonald
> <jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>
> <mailto:jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>>
> <mailto:jmacdon at med.umich.edu
> <mailto:jmacdon at med.umich.edu> <mailto:jmacdon at med.umich.edu
> <mailto:jmacdon at med.umich.edu>>>>
>
> wrote:
>
> Hi Bala,
>
> Try this:
>
> eset <- justRMA(cdfname = "ecoliasv2cdf")
>
> Best,
>
> Jim
>
>
>
> Balasubramanian Ganesan wrote:
>
> Hello BioC team
> I have downloaded an old microarray expression
> data set for
> analysis from
> NCBI's GEO database.
> When I try to normalize the data in R2.9 (OS X
> Leopard) using
> justRMA() the
> normalization fails as it is looking for a library
> file
> called
> "ecoliantisensecdf"
> and cannot find it.
> However if try to download the corresponding
> library file
> from
> Affy''s
> website I only get a library file called
> "Ecoli_ASv2" and not
> "ecoliantisense".
> Affymetrix insists that this library file works
> fine with the
> cel files I
> have inside their software (Expression console)
> and that the
> array layouts
> of the older ecoliantisense and the newer
> Ecoli_ASv2 are the
> same. But I
> have had no luck trying to use the new library in R.
> Is there a possible way to resolve this issue?
> Thank you inn advance.
> BALA
>
> [[alternative HTML version deleted]]
>
>
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>
> -- James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>
> **********************************************************
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> not be used for urgent or sensitive issues
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>
--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
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