[BioC] oligo package

James W. MacDonald jmacdon at uw.edu
Thu Dec 6 20:13:36 CET 2012 


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 “GeneFeatureSet” object: 1: sampleNames differ between assayData and phenoData
> invalid class “GeneFeatureSet” 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
>
> --
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>
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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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