Dear Jim
Sorry, I did not quite understand your earlier comment and had no specific
intention of getting things off the mailing list - probably a reflex to just
hit "reply" instead of "reply all". My apologies to you and other list
members.
Just a note that as to why I misunderstood your earlier comment - it didn't
address me, as I saw it.
About the chips: ah, sorry. This is something I have done earlier for a
different chip with two diff. cdf libraries but I never realized that this
issue was causing the troubles.
Thanks for bringing this to my attention.
BALA

On Mon, Mar 22, 2010 at 12:27 PM, James W. MacDonald
<jmacdon@med.umich.edu>wrote:

> 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@med.umich.edu <mailto:jmacdon@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@med.umich.edu <mailto:jmacdon@med.umich.edu>
>>        <mailto:jmacdon@med.umich.edu <mailto: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>
>>        <mailto:jmacdon@med.umich.edu <mailto:jmacdon@med.umich.edu>>
>>               <mailto:jmacdon@med.umich.edu
>>        <mailto:jmacdon@med.umich.edu> <mailto: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
>>
>>                             [[alternative HTML version deleted]]
>>
>>
>>                      _______________________________________________
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>>        <mailto:Bioconductor@stat.math.ethz.ch>
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>>                      <mailto:Bioconductor@stat.math.ethz.ch
>>        <mailto:Bioconductor@stat.math.ethz.ch>
>>               <mailto:Bioconductor@stat.math.ethz.ch
>>        <mailto:Bioconductor@stat.math.ethz.ch>>>
>>
>>                      https://stat.ethz.ch/mailman/listinfo/bioconductor
>>                      Search the archives:
>>
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>>
>>
>>  **********************************************************
>>                  Electronic Mail is not secure, may not be read every
>>        day, and
>>               should
>>                  not be used for urgent or sensitive issues
>>
>>
>>
>>           --     James W. MacDonald, M.S.
>>           Biostatistician
>>           Hildebrandt Lab
>>           8220D MSRB III
>>           1150 W. Medical Center Drive
>>           Ann Arbor MI 48109-5646
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>>
>>           **********************************************************
>>           Electronic Mail is not secure, may not be read every day, and
>>        should
>>           not be used for urgent or sensitive issues
>>
>>
>>
>>    --     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
>>
>>    **********************************************************
>>    Electronic Mail is not secure, may not be read every day, and should
>>    not be used for urgent or sensitive issues
>>
>>
>>
> --
> 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
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues
>

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