[BioC] problems with gcrma just.gcrma

[Elisabetta Manduchi]

Hi Jim,
thanks for your feedback. They appear to be all .CEL files:

> cel.files
  [1] 
"../../data_repository/quantifications/NDminus_E15.5_Pan_11-13-03_MGU74Av2.CEL"
  [2] "../../data_repository/quantifications/NDminus_E18_Pan_MGU74Av2.CEL"
  [3] "../../data_repository/quantifications/NDminus_P1_Pan_MGU74Av2.CEL"
  [4] 
"../../data_repository/quantifications/NDminus_P1_PanIslet_MGU74Av2_3-4-03.CEL"
  [5] 
"../../data_repository/quantifications/CGC_NDmutant_John_Sample_4_MGU74Av2.CEL"
  [6] 
"../../data_repository/quantifications/NDplus_E15.5_Pan_11-13-03_MGU74Av2.CEL"
  [7] 
"../../data_repository/quantifications/NDplus_E18_Pan_MGU74Av2rescan.CEL"
  [8] "../../data_repository/quantifications/NDplus_P1_Pan_MGU74Av2.CEL"
  [9] 
"../../data_repository/quantifications/NDplus_P1_PanIslet_MGU74Av2_3-4-03.CEL"
[10] 
"../../data_repository/quantifications/CGC_Wild_John_Sample_3_MGU74Av2.CEL"
>

I've checked them one by one and they are indeed .CEL. I didn't use 
list.celfiles because I'm only using a subset of the .CEL files contained 
in this directory.
Elisabetta

---

On Mon, 4 Dec 2006, James W. MacDonald wrote:

> Hi Elisabetta,
>
> Elisabetta Manduchi wrote:
>> Hello,
>> I'm trying to use just.gcrma with data from Affy MGU74Av2 and am getting 
>> the error at the bottom of what's copied below re read.probematrix. I'm 
>> running version 2.4.0 of R and gcrma version 2.6.0. The mgu74av2 
>> packages being downloaded are version 1.14.0.
>> Can anybody advice on what I can do to overcome this?
>
> That error usually means that you are not pointing to celfiles with your 
> filenames argument. What do you get if you type
>
> cel.files
>
> at the R prompt? It is often easier to use filenames=list.celfiles().
>
> Best,
>
> Jim
>
>
>> Thanks,
>> Elisabetta
>> ---
>> 
>>> data.gcrma<-just.gcrma(filenames=cel.files, type=c("fullmodel"), 
>>> normalize=T, optimize.by=c("memory"), fast=T, 
>>> samepleNames=sample.names)
>> 
>> 
>> Computing affinities[1] "Checking to see if your internet connection 
>> works..."
>> trying URL 
>> 'http://bioconductor.org/packages/1.9/data/annotation/bin/windows/contrib/2.4/mgu74av2cdf_1.14.0.zip'
>> Content type 'application/zip' length 1340750 bytes
>> opened URL
>> downloaded 1309Kb
>> 
>> package 'mgu74av2cdf' successfully unpacked and MD5 sums checked
>> 
>> The downloaded packages are in
>>          C:\Documents and Settings\Elisabetta Manduchi\Local 
>> Settings\Temp\Rtmpc7v1qb\downloaded_packages
>> updating HTML package descriptions
>> [1] "Checking to see if your internet connection works..."
>> trying URL 
>> 'http://bioconductor.org/packages/1.9/data/annotation/bin/windows/contrib/2.4/mgu74av2probe_1.14.0.zip'
>> Content type 'application/zip' length 2396326 bytes
>> opened URL
>> downloaded 2340Kb
>> 
>> package 'mgu74av2probe' successfully unpacked and MD5 sums checked
>> 
>> The downloaded packages are in
>>          C:\Documents and Settings\Elisabetta Manduchi\Local 
>> Settings\Temp\Rtmpc7v1qb\downloaded_packages
>> updating HTML package descriptions
>> .Done.
>> Error in read.probematrix(filenames = filenames, which = "pm", cdfname = 
>> cdfname) :
>>          VECTOR_ELT() can only be applied to a 'list', not a 'symbol'
>> ---
>> 
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>
>
> -- 
> James W. MacDonald
> University of Michigan
> Affymetrix and cDNA Microarray Core
> 1500 E Medical Center Drive
> Ann Arbor MI 48109
> 734-647-5623
>
>
>
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