Dear list,

 

I have performed a GCRMA normalization with my Affy data, and then tried the
'nsFilter' function from the 'genefilter' package but got an error message
as follows.  Help much appreciated.  Thanks.

 

Thomas

 

> library(gcrma)

> library(genefilter)

> s.names <- letters[1:10]

> exset <- justGCRMA(sampleNames = s.names)

> exset

ExpressionSet (storageMode: lockedEnvironment)

assayData: 54675 features, 10 samples 

  element names: exprs, se.exprs 

phenoData

  rowNames: a, b, ..., j (10 total)

  varLabels and varMetadata:

    sample: arbitrary numbering

featureData

  featureNames: 1007_s_at, 1053_at, ..., AFFX-TrpnX-M_at (54675 total)

  varLabels and varMetadata: none

experimentData: use 'experimentData(object)'

Annotation [1] "hgu133plus2"

 

> filterAns <- nsFilter(exset)

Error: no 'dimnames' attribute for array

 

> sessionInfo()

R version 2.5.0 (2007-04-23) 

i386-pc-mingw32 

 

locale:

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

 

attached base packages:

[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"    

[7] "datasets"  "methods"   "base"     

 

other attached packages:

     hgu133plus2       genefilter         survival hgu133plus2probe 

        "1.16.0"         "1.14.1"           "2.32"         "1.16.0" 

  hgu133plus2cdf            gcrma      matchprobes             affy 

        "1.16.0"          "2.8.1"          "1.8.1"         "1.14.1" 

          affyio          Biobase 

         "1.4.0"         "1.14.0"

 

 

Thomas Lo

 

Department of Anatomical & Cellular Pathology

The Chinese University of Hong Kong

 


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