[BioC] oneChannelGUI and Affymetrix 1.0 ST arrays

[cstrato]

Dear Raffaele,

I do not think that this is an error from APT tools unable to read some 
of the CEL files.

The output:
    Wrong number of cells: Expecting: 1178100 and 2A.CEL has: 1102500
suggests that the PGF-file for HuGene-1_1-st-v1 was used and not the 
PGF-file for HuGene-1_0-st-v1:

    HuGene-1_0-st-v1 has a size of 1050 x 1050 = 1102500
    HuGene-1_1-st-v1 has a size of 1190 x 990  = 1178100

Thus for 2A.CEL APT seems to require the PGF-file for HuGene-1_0-st-v1.

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
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On 6/9/10 2:54 PM, rcaloger wrote:
> Il 09/06/2010 12:00, bioconductor-request at stat.math.ethz.ch ha scritto:
>> Steve Taylor<stephen.taylor at imm.ox.ac.uk>
> 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
>
> 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
>
> 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