[BioC] Ecoli antisense library

[James MacDonald]

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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>> 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
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