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@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@med.umich.edu <mailto:jmacdon@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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