[BioC] oneChannelGUI and Affymetrix 1.0 ST arrays

[Steve Taylor]

Hi,

I am trying use oneChannelGUI to analyse some Affymetrix 1.0 ST arrays but I can't read in the data. I have two questions:

1) Why is this not working in OneChannelGUI?
2) If I can't get this to work, what are the best alternatives to read and normalise this data (to be subsequently analysed by LIMMA)?

I have 12 CEL files:

1A.CEL
1B.CEL
2A.CEL
2B.CEL
T10.CEL
T11.CEL
T12.CEL
T3.CEL
T4.CEL
T5.CEL
T6.CEL
T7.CEL
T8.CEL
T9.CEL


Using OneChannelGUI, when I try and read in the CEL files using rma-sketch or iter-plier I get

Error in read.table(paste(tempOut,"/",content.outDir[tempOut1],sep=""),:
no lines available in input

and then various other errors in the Tk window. In my terminal window I get:

Gene level probe sets summary started
Read 12 cel files from: target327b23c6
Wrong number of cells: Expecting: 1178100 and 1A.CEL has: 1102500
Wrong number of cells: Expecting: 1178100 and 2A.CEL has: 1102500

FATAL ERROR: Can't read file: 3.CEL

Gene level probe sets summary ended
Error in as.matrix(my.exons) :
   no function to return from, jumping to top level


> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu

locale:
  [1] LC_CTYPE=en_GB.ISO-8859-1       LC_NUMERIC=C
  [3] LC_TIME=en_GB.ISO-8859-1        LC_COLLATE=en_GB.ISO-8859-1
  [5] LC_MONETARY=C                   LC_MESSAGES=en_GB.ISO-8859-1
  [7] LC_PAPER=en_GB.ISO-8859-1       LC_NAME=C
  [9] LC_ADDRESS=C                    LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.ISO-8859-1 LC_IDENTIFICATION=C

attached base packages:
[1] tools     tcltk     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] oneChannelGUI_1.12.5 preprocessCore_1.8.0 GOstats_2.12.0
  [4] RSQLite_0.8-4        DBI_0.2-5            graph_1.24.4
  [7] Category_2.12.0      AnnotationDbi_1.8.1  tkWidgets_1.24.0
[10] DynDoc_1.24.0        widgetTools_1.24.0   affylmGUI_1.20.0
[13] affyio_1.14.0        affy_1.24.2          limma_3.2.2
[16] Biobase_2.6.1

loaded via a namespace (and not attached):
[1] annotate_1.24.1   genefilter_1.28.2 GO.db_2.3.5       GSEABase_1.8.0
[5] RBGL_1.22.0       splines_2.10.1    survival_2.35-8   XML_2.6-0
[9] xtable_1.5-6

Thanks very much for any help,

Steve