[BioC] Agi4x44PreProcess package: Error in build.est

[Jon Mohl]

Francois,

Here is the results...

> dim(targets)
[1] 3 4
> dim(tdPROC)
[1] 41093     3

And here are the filenames and the start of my tdPROC$G for comparison as well.

> targets
  Slide.Number
1            1
2            2
3            3


  FileName
1 /Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilent_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_1_006_DS_EP
2 /Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilent_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_2_008_BR_LP
3 /Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilent_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_3_005_EC_NP
  Treatment GErep
1        EP     1
2        LP     2
3        NP     3
> colnames(tdPROC$G)
[1] "/Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilent_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_1_006_DS_EP"
[2] "/Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilent_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_2_008_BR_LP"
[3] "/Microarray_raw_data_Protein_Genomic/Agilent_Genomic/Tissue_Agilent_Genomic/US23502379_251485040308_S01_GE1-v5_91_0806_1_3_005_EC_NP"

Thanks for trying to help,

Jon Mohl

On Fri, Oct 7, 2011 at 10:53 AM, Francois Pepin
<francois.pepin at sequentainc.com> wrote:
> Hi Jon,
>
> You would have to give us some more information about your code.
>
> The error message indicates that you don't have the same number of samples data (tdPROC: colnames RGlist$G) as you have information about (targets: pData(targets)).
>
> What sare the result of:
> dim(tdPROC)
> dim(targets)
>
> Francois
>
> On Oct 7, 2011, at 8:03 , Jon Mohl wrote:
>
>> Hello,
>>
>> I am currently getting a error when trying to use the build.est
>> function of the Agi4x44PreProcess package.  The error is as follows:
>>
>> Error in build.eset(tdPROC, targets, makePLOT = FALSE,
>> annotation.package = "hgug4112a.db") :
>>  rownames in pData(targets) different from colnames RGlist$G
>>
>> Here is the command I have given:
>>
>> esetPROC = build.eset(tdPROC, targets, makePLOT = FALSE,
>> annotation.package="hgug4112a.db")
>>
>>
>> I have followed the example within the Agi4x44PreProcess.pdf manual,
>> and thus far this is the only problem I have run into.  For reference,
>> I am running R 2.10.1.
>>
>> Thanks for your help,
>>
>> Jon Mohl
>>
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>
>
>