[BioC] oneChannelGUI and Affymetrix 1.0 ST arrays

[rcaloger]

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
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
        raffaele[dot]calogero[at]gmail[dot]com
www:   http://www.bioinformatica.unito.it
Info: http://publicationslist.org/raffaele.calogero