[BioC] oneChannelGUI and Affymetrix 1.0 ST arrays

Mon Jun 14 17:59:47 CEST 2010

Hi Steve,
many thanks for the bug report.
The bug in the usage of iter-plier summarization for gene arrays is 
fixed in oneChannelGUI 1.14.4, which should be available in a 24 hours 
on the bioconductor web
Cheer
Raffaele

Il 14/06/2010 14:52, Steve Taylor ha scritto:
> Hi,
>
>> 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.
>
> Thanks for your advice.
>
> I upgraded to the latest version of R/OneChannelGUI and it is 
> basically working, though there seem to be a bug using Iter-plier.
>
>  Here is the output when loading in the data using RMA-Sketch
>>
> Gene level probe sets summary started
> Read 12 cel files from: target79e2a9e3
> Opening clf file: HuGene-1_0-st-v1.r4.clf
> Opening pgf file: HuGene-1_0-st-v1.r4.pgf
> Expecting 1 iteration.
> Doing iteration: 1
> Opening clf file: HuGene-1_0-st-v1.r4.clf
> Opening pgf file: HuGene-1_0-st-v1.r4.pgf
> Loading 33297 probesets and 804955 probes.
> Reading 12 cel files............Done.
> Processing Probesets......................Done.
> Flushing output reporters. Finalizing output.
> Done.
> Cleaning up.
> Done.
> Run took approximately: 0.96 minute.
>
> But if I use Iter-plier
>
> Gene level probe sets summary started
> Read 12 cel files from: target1d4ed43b
> Opening bgp file:
> terminate called after throwing an instance of 'std::ios_base::failure'
>   what():  basic_filebuf::underflow error reading the file
>
> Gene level probe sets summary ended
> Error in as.matrix(my.exons) :
>   no function to return from, jumping to top level
> In addition: Warning messages:
> 1: In file(file, "rt") : only first element of 'description' argument 
> used
> 2: In file(file, "rt") : only first element of 'description' argument 
> used
>
> Also, is there anyway to change the font size in the QC steps (e.g. 
> PCA plot/Dendrogram display)?
>
> Thanks again,
>
> Steve
>
>
>> 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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