If you can guarantee that the order of samples in your txt file is the same
as in your 'celfiles' variables, you should be okay with:

pd <- read.table("phenodata.txt"**)
pd <- as(pd, "AnnotatedDataFrame")
TFdata <- read.celfiles(**celfiles)
sampleNames(pd) <- sampleNames(TFdata)
phenoData(pd) <- pd

b


On 6 December 2012 19:13, James W. MacDonald <jmacdon@uw.edu> wrote:

>
>
> On 12/6/2012 1:59 PM, Bruno [guest] wrote:
>
>> ok sorry ill copy and past all the steps i've done after loading the
>> "oligo" package.
>> Thanks a lot
>>
>> celfiles<-list.celfiles()
>>
>>> celfiles
>>>
>>   [1] "Titan_0026_838M_Freeman_838M_**A1_A05.CEL"
>>  "Titan_0026_838M_Freeman_838M_**A1_E09.CEL"
>>  "Titan_0026_838M_Freeman_838M_**A10_B07.CEL"
>>   [4] "Titan_0026_838M_Freeman_838M_**A2_B05.CEL"
>>  "Titan_0026_838M_Freeman_838M_**A3_C05.CEL"
>>  "Titan_0026_838M_Freeman_838M_**A3_F09.CEL"
>>   [7] "Titan_0026_838M_Freeman_838M_**A4_D05.CEL"
>>  "Titan_0026_838M_Freeman_838M_**A5_E05.CEL"
>>  "Titan_0026_838M_Freeman_838M_**A6_F05.CEL"
>> [10] "Titan_0026_838M_Freeman_838M_**A7_G05.CEL"
>>  "Titan_0026_838M_Freeman_838M_**A8_H05.CEL"
>>  "Titan_0026_838M_Freeman_838M_**A9_A07.CEL"
>> [13] "Titan_0026_838M_Freeman_838M_**B1_C07.CEL"
>>  "Titan_0026_838M_Freeman_838M_**B1_G09.CEL"
>>  "Titan_0026_838M_Freeman_838M_**B10_D09.CEL"
>> [16] "Titan_0026_838M_Freeman_838M_**B2_D07.CEL"
>>  "Titan_0026_838M_Freeman_838M_**B3_E07.CEL"
>>  "Titan_0026_838M_Freeman_838M_**B4_F07.CEL"
>> [19] "Titan_0026_838M_Freeman_838M_**B4_H09.CEL"
>>  "Titan_0026_838M_Freeman_838M_**B5_G07.CEL"
>>  "Titan_0026_838M_Freeman_838M_**B6_H07.CEL"
>> [22] "Titan_0026_838M_Freeman_838M_**B7_A09.CEL"
>>  "Titan_0026_838M_Freeman_838M_**B8_B09.CEL"
>>  "Titan_0026_838M_Freeman_838M_**B9_C09.CEL"
>>
>>> pd<-read.table("phenodata.txt"**)
>>> pd<-as(pd, "AnnotatedDataFrame")
>>> TFdata<-read.celfiles(**celfiles, phenoData=pd)
>>>
>> Platform design info loaded.
>> Reading in : Titan_0026_838M_Freeman_838M_**A1_A05.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A1_E09.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A10_B07.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A2_B05.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A3_C05.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A3_F09.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A4_D05.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A5_E05.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A6_F05.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A7_G05.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A8_H05.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**A9_A07.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B1_C07.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B1_G09.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B10_D09.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B2_D07.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B3_E07.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B4_F07.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B4_H09.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B5_G07.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B6_H07.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B7_A09.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B8_B09.CEL
>> Reading in : Titan_0026_838M_Freeman_838M_**B9_C09.CEL
>>
>> Error in validObject(out) :
>>    invalid class тАЬGeneFeatureSetтА  object: 1: sampleNames differ
>> between assayData and phenoData
>> invalid class тАЬGeneFeatureSetтА  object: 2: sampleNames differ between
>> phenoData and protocolData
>>
>
> OK, this is a bit better, although it is still a mystery what is in your
> phenoData. However, the error messages say what the problem is - the
> phenoData object that you are trying to put in your GeneFeatureSet is
> incompatible.
>
> Now I am no expert on the intricacies of the phenoData slot, because I
> actually never use it. So unless you are planning on doing things with the
> phenoData slot, you can just go forward without specifying it directly:
>
> TFdata<-read.celfiles(**celfiles) ## side note - spaces are good
>
>
> However, it isn't difficult to see what is expected. We can just open up
> an existing ExpressionSet (which GeneFeatureSet is a subset of), and see
> what is in there:
>
> > library(affydata)
> > data(Dilution)
> > pData(phenoData(Dilution))
> liver sn19 scanner
> 20A 20 0 1
> 20B 20 0 2
> 10A 10 0 1
> 10B 10 0 2
> > sampleNames(Dilution)
> [1] "20A" "20B" "10A" "10B"
>
> So there are four samples here, and the row names of the phenoData match
> those sample names. So the first step for you is to ensure that the row
> names of the data.frame you are using to create the phenoData are identical
> to the sampleNames that will result (e.g., they should be identical to your
> celfiles variable).
>
> Best,
>
> Jim
>
>
>
>>   -- output of sessionInfo():
>>
>>
>> sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
>>
>> [5] LC_TIME=English_United Kingdom.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] pd.hugene.1.1.st.v1_3.8.0 RSQLite_0.11.2            DBI_0.2-5
>>         oligo_1.22.0              Biobase_2.18.0
>>  oligoClasses_1.20.0
>> [7] BiocGenerics_0.4.0        BiocInstaller_1.8.3
>>
>>
>> loaded via a namespace (and not attached):
>>   [1] affxparser_1.30.0     affyio_1.26.0         Biostrings_2.26.2
>> bit_1.1-9             codetools_0.2-8       ff_2.2-10
>> foreach_1.4.0
>>   [8] GenomicRanges_1.10.5  IRanges_1.16.4        iterators_1.0.6
>> parallel_2.15.1       preprocessCore_1.20.0 splines_2.15.1
>>  stats4_2.15.1
>> [15] tools_2.15.1          zlibbioc_1.4.0
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
>> ______________________________**_________________
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
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