Hi Steve,
  thanks for the prompt answer.
Actually you are using R 2.10.1 and the lastest oneChannelGUI is running 
on R 2.11

You need to update R and oneChannelGUi using the code at:
http://www.bioinformatica.unito.it/oneChannelGUI/ 
<http://www.bioinformatica.unito.it/oneChannelGUI/>

The error you get is due to the fact that in the new release of 
oneChannelGUI, gene array in the 96 plate format can be also run and 
those arrays use a different set of library files, which are now 
embedded in the library files you are downloading from my web site when 
you run the first time an analysis with APT tools.
In the previous version of oneChannelGUI this was not present and this 
produces the error you have found.

Please let me know if everything is working after the new installation 
of R and bioconductor.
Cheers
Raffaele

Il 09/06/2010 15:06, Steve Taylor ha scritto:
> 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
>


-- 

----------------------------------------
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@unito.it
        raffaele[dot]calogero[at]gmail[dot]com
www:   http://www.bioinformatica.unito.it
Info: http://publicationslist.org/raffaele.calogero


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