[BioC] oneChannelGUI and Affymetrix 1.0 ST arrays

[Steve Taylor]

DearRaffaele,

>>
> Dear Steve,
> there is some problem with the cel files you are using as indicated by
> the error:
>
> Wrong number of cells: Expecting: 1178100 and 1A.CEL has: 1102500
> Wrong number of cells: Expecting: 1178100 and 2A.CEL has: 1102500
>
> This is an error from APT tools which are unable to read some of your
> CEL file.
> Furthermore, you must have an error in the target file used to load the
> data set, since
> the software try to read CEL file 3.CEL
>
> FATAL ERROR: Can't read file: 3.CEL

This file definitely exists and is defined in the targets file...

>
> but this is not present in the list of arrays you have indicated in the
> mail.
>
> To help you in solving your problem I need to know which are the arrays
> under analysis:
> human, mouse, rat
> gene, exon arrays
>

Human Affymetrix Gene 1.0 ST array

> 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
> affylmGUIenvironment$libDirLocation
[1] "/package/R/2.10.1/lib64/R/library/oneChannelGUI/affylibs"
> affylmGUIenvironment$aptDir
[1] "/package/apt/1.10.0-20080710"

Thanks,

Steve



> To have an idea of the installation please write in the main R window:
> sessionInfo()
> affylmGUIenvironment$libDirLocation
> affylmGUIenvironment$aptDir
>
> and send the output to me.
> Cheers
> Raffaele
>
>
>
>> 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)?
>
>> 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