[BioC] oneChannelGUI and Affymetrix 1.0 ST arrays

[rcaloger]

Hi Christian,
after Steve, sent me the sessionInfo() results, it came out that he was 
using onechannelGUI from Bioconductor release 2.5. oneChannelGUI 
released with Bioconductor 2.6 now allows to handle both normal gene 
arrays and 96 format gene arrays. For this reason in the library files 
that are associated to oneChannelGUI there are two different types of 
Gene array library files:
HuGene-1_0-st-v1 and HuGene-1_1-st-v1
So I told Steve to upgrade the oneChannelGUI installation and the 
problem will be solved.
Cheers
Raffaele



Il 09/06/2010 21:23, cstrato ha scritto:
> 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
> _._._._._._._._._._._._._._._._._._
>
>
> 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
>


-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
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email: raffaele.calogero at unito.it
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