[BioC] Ecoli antisense library

[James W. MacDonald]

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>> 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>>>
>         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
> 
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> 
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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
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