[BioC] oneChannelGUI and Affymetrix 1.0 ST arrays

[Steve Taylor]

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
>>
>
>