[BioC] xps rma() with HuGene-1_0-st-v1 on 64-bit architecture
Tim Rayner
tfrayner at gmail.com
Wed Feb 18 11:45:32 CET 2009
Dear Christian,
Thank you very much for your help - reverting to the older r3 files
does indeed solve the problem. I'll look forward to hearing about the
new version of the xps package, and I'd be more than happy to help
test it if needed.
Best regards,
Tim
2009/2/17 cstrato <cstrato at aon.at>:
> Dear Tim,
>
> First, I am glad to hear that my package works on 64-bit OS w/o problems.
>
> Luckily, the solution to your problem is simple. Please use the following
> pgf and clf files in your code to create xps.scheme:
> - HuGene-1_0-st-v1.r3.clf
> - HuGene-1_0-st-v1.r3.pgf
>
> The reason is as follows:
> About two weeks ago Affymetrix has updated the pgf file to allow customers
> to use HuGene as a cheaper exon array. For this purpose, they have created
> an additional "HuGene-1_0-st-v1.na27.hg18.probeset.csv" file and have
> changed the probesets in the *.pgf file. Instead of "transcript_cluster_id"
> the probes are now mapped to "probeset_id" of the new probeset annotation
> file. For this reason xps recognizes only the 57 affx-controls when parsing
> the *.pgf file, and thus only these 57 controls will be summarized.
>
> I am currently in the process to update my package to allow using HuGene
> arrays as exon arrays, and I will inform you once I have uploaded the new
> version. Until then I must ask you to use the older *.r3.pgf file.
>
> 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
> _._._._._._._._._._._._._._._._._._
>
>
> Tim Rayner wrote:
>>
>> Hi,
>>
>> I'm seeing what appears to be odd behaviour from the xps rma() method
>> when trying to summarize a small test dataset from the
>> HuGene-1_0-st-v1 array. The oddness is that whatever options I pass to
>> rma(), I only ever get summary data for 57 probe sets back (obviously
>> I'd expect rather more than that).
>>
>> I'm using 64-bit Mac OSX, and I believe I've installed everything
>> correctly and imported the probe annotation from the latest chip
>> library files on Affy's web site. I did have to compile ROOT from
>> source to support the 64-bit architecture, but that went pretty
>> smoothly. After some hours of poking through the xps code I'm a little
>> suspicious about the probe masking, but not much wiser, I'm afraid.
>>
>> I should just briefly mention that I can run rma over the same data
>> set by using the oligo package, so I think the data files are fine.
>>
>> Attached is a sample session, which I've just run from scratch to
>> confirm the problem, and my sessionInfo. I'm wondering if anyone else
>> has seen this, or if I've just made some fundamental error.
>>
>> Many thanks,
>>
>> Tim Rayner
>>
>>
>>
>> #############################################
>> ## sessionInfo():
>>
>>
>>>
>>> sessionInfo()
>>>
>>
>> R version 2.8.1 Patched (2009-01-19 r47650)
>> i386-apple-darwin9.6.0
>>
>> locale:
>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>>
>> attached base packages:
>> [1] tools stats graphics grDevices utils datasets methods
>> [8] base
>>
>> other attached packages:
>> [1] Biobase_2.2.2 xps_1.2.5
>>
>> loaded via a namespace (and not attached):
>> [1] tcltk_2.8.1
>>
>>
>>
>> ##############################################
>> ## Session commands:
>> library('xps')
>> celdir=getwd()
>> celfiles=list.files(pattern='.*.CEL')
>> libdir <- '/Users/tfr23/Documents/resources/HuGene-1_0/'
>> xps.scheme <- import.genome.scheme(filename='HuGene-1_0-st-v1-r4',
>> filedir=libdir,
>> layoutfile=paste(libdir,
>> 'HuGene-1_0-st-v1.r4.clf',
>> sep=''),
>> schemefile=paste(libdir,
>> 'HuGene-1_0-st-v1.r4.pgf',
>> sep=''),
>> transcript=paste(libdir,
>>
>> 'HuGene-1_0-st-v1.na27.hg18.transcript.csv',
>> sep=''),
>> verbose=TRUE)
>>
>> xps.cel<-import.data(xps.scheme, 'HuGeneCelData', celdir=celdir,
>> celfiles=celfiles)
>>
>> xps.cel<-attachInten(xps.cel)
>>
>> xps.rma <- rma(xps.cel,
>> filename='HuGeneMixRMAMetacore',
>> exonlevel='metacore+affx',
>> background='antigenomic',
>> normalize=TRUE)
>>
>> ######################################
>> ## Session output:
>>
>> Welcome to xps version 1.2.5
>> an R wrapper for XPS - eXpression Profiling System
>> (c) Copyright 2001-2009 by Christian Stratowa
>>
>> Creating new file
>> </Users/tfr23/Documents/resources/HuGene-1_0/HuGene-1_0-st-v1-r4.root>...
>> Importing
>> </Users/tfr23/Documents/resources/HuGene-1_0/HuGene-1_0-st-v1.r4.clf>
>> as <HuGene-1_0-st-v1.cxy>...
>> <1102500> records imported...Finished
>> New dataset <HuGene-1_0-st-v1> is added to Content...
>> Importing
>> </Users/tfr23/Documents/resources/HuGene-1_0/HuGene-1_0-st-v1.na27.hg18.transcript.csv>
>> as <HuGene-1_0-st-v1.ann>...
>> Number of transcripts is <33297>.
>> <33297> records read...Finished
>> <33297> records imported...Finished
>> Importing
>> </Users/tfr23/Documents/resources/HuGene-1_0/HuGene-1_0-st-v1.r4.pgf>
>> as <HuGene-1_0-st-v1.scm>...
>> Reading data from input file...
>> Number of probesets is <257430>.
>> Note: Number of annotated probesets <33297> is not equal to number of
>> probesets <257430>.
>> <257430> records read...Finished
>> Sorting data for probeset_type and position...
>> Total number of controls is <4371>
>> Note: no data for probeset type: control->chip...
>> Filling trees with data for probeset type: normgene, rescue...
>> Filling trees with data for probeset type: control->bgp...
>> Filling trees with data for probeset type: control->affx...
>> <33252> probeset tree entries read...Finished
>> Number of control->affx probesets is <57>.
>> Filling trees with data for probeset type: main...
>> Filling trees with data for non-annotated probesets...
>> <861493> records imported...Finished
>> <257430> total transcript units imported.
>> Genome cell statistics:
>> Number of unit cells: minimum = 1, maximum = 1189
>> Opening file
>> </Users/tfr23/Documents/resources/HuGene-1_0/HuGene-1_0-st-v1-r4.root>
>> in <READ> mode...
>> Creating new file
>> </Users/tfr23/Documents/affytest/HuGeneCelData_cel.root>...
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 020206A CD8 -
>> 090213.CEL> as <Affy 0104 - 020206A CD8 - 090213.cel>...
>> hybridization statistics:
>> 1 cells with minimal intensity 23
>> 1 cells with maximal intensity 35735
>> New dataset <DataSet> is added to Content...
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 020305 CD8 -
>> 090213.CEL> as <Affy 0104 - 020305 CD8 - 090213.cel>...
>> hybridization statistics:
>> 2 cells with minimal intensity 20
>> 1 cells with maximal intensity 24768
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 030804 CD8 -
>> 090213.CEL> as <Affy 0104 - 030804 CD8 - 090213.cel>...
>> hybridization statistics:
>> 6 cells with minimal intensity 25
>> 1 cells with maximal intensity 38526
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 040107 CD8 -
>> 090213.CEL> as <Affy 0104 - 040107 CD8 - 090213.cel>...
>> hybridization statistics:
>> 2 cells with minimal intensity 22
>> 1 cells with maximal intensity 20150
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 061004 CD8 -
>> 090213.CEL> as <Affy 0104 - 061004 CD8 - 090213.cel>...
>> hybridization statistics:
>> 2 cells with minimal intensity 20
>> 1 cells with maximal intensity 21650
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 070205 CD8 -
>> 090213.CEL> as <Affy 0104 - 070205 CD8 - 090213.cel>...
>> hybridization statistics:
>> 2 cells with minimal intensity 21
>> 1 cells with maximal intensity 23005
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 090305 CD8 -
>> 090213.CEL> as <Affy 0104 - 090305 CD8 - 090213.cel>...
>> hybridization statistics:
>> 22 cells with minimal intensity 21
>> 1 cells with maximal intensity 21205
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 110806B CD8 -
>> 090213.CEL> as <Affy 0104 - 110806B CD8 - 090213.cel>...
>> hybridization statistics:
>> 1 cells with minimal intensity 21
>> 1 cells with maximal intensity 22958
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 150107 CD8 -
>> 090213.CEL> as <Affy 0104 - 150107 CD8 - 090213.cel>...
>> hybridization statistics:
>> 2 cells with minimal intensity 19
>> 1 cells with maximal intensity 23606
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 150405 CD8 -
>> 090213.CEL> as <Affy 0104 - 150405 CD8 - 090213.cel>...
>> hybridization statistics:
>> 4 cells with minimal intensity 24
>> 1 cells with maximal intensity 24268
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 190706 CD8 -
>> 090213.CEL> as <Affy 0104 - 190706 CD8 - 090213.cel>...
>> hybridization statistics:
>> 6 cells with minimal intensity 21
>> 1 cells with maximal intensity 22769
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 - 300605 CD8 -
>> 090213.CEL> as <Affy 0104 - 300605 CD8 - 090213.cel>...
>> hybridization statistics:
>> 2 cells with minimal intensity 20
>> 1 cells with maximal intensity 22309
>> Importing </Users/tfr23/Documents/affytest/Affy 0104 -040205 CD8 -
>> 090213.CEL> as <Affy 0104 -040205 CD8 - 090213.cel>...
>> hybridization statistics:
>> 1 cells with minimal intensity 23
>> 1 cells with maximal intensity 22497
>> Creating new file
>> </Users/tfr23/Documents/affytest/HuGeneMixRMAMetacore.root>...
>> Opening file
>> </Users/tfr23/Documents/resources/HuGene-1_0/HuGene-1_0-st-v1-r4.root>
>> in <READ> mode...
>> Preprocessing data using method <preprocess>...
>> Background correcting raw data...
>> setting selector mask for typepm <8252>
>> calculating background for <Affy 0104 - 020206A CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 1378 cells with maximal intensity 151.284
>> calculating background for <Affy 0104 - 020305 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 2 cells with maximal intensity 75.9992
>> calculating background for <Affy 0104 - 030804 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 28 cells with maximal intensity 122.454
>> calculating background for <Affy 0104 - 040107 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 13 cells with maximal intensity 154.02
>> calculating background for <Affy 0104 - 061004 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 47 cells with maximal intensity 101.165
>> calculating background for <Affy 0104 - 070205 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 25 cells with maximal intensity 94.408
>> calculating background for <Affy 0104 - 090305 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 220 cells with maximal intensity 52.9483
>> calculating background for <Affy 0104 - 110806B CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 97 cells with maximal intensity 136.739
>> calculating background for <Affy 0104 - 150107 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 1055 cells with maximal intensity 105.265
>> calculating background for <Affy 0104 - 150405 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 36 cells with maximal intensity 128.385
>> calculating background for <Affy 0104 - 190706 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 957 cells with maximal intensity 135.396
>> calculating background for <Affy 0104 - 300605 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 865 cells with maximal intensity 49.4309
>> calculating background for <Affy 0104 -040205 CD8 - 090213.cel>...
>> background statistics:
>> 1097995 cells with minimal intensity 0
>> 650 cells with maximal intensity 140.053
>> Normalizing raw data...
>> normalizing data using method <quantile>...
>> setting selector mask for typepm <8252>
>> finished filling <13> arrays. 90213>...
>> finished filling <13> trees. 090213.cqu>...
>> Converting raw data to expression levels...
>> summarizing with <medianpolish>...
>> setting selector mask for typepm <8252>
>> setting selector mask for typepm <8252>
>> calculating expression for <57> of <257430> units...Finished.
>> expression statistics:
>> minimal expression level is <19.8498>
>> maximal expression level is <8953.24>
>> preprocessing finished.
>> Opening file
>> </Users/tfr23/Documents/resources/HuGene-1_0/HuGene-1_0-st-v1-r4.root>
>> in <READ> mode...
>> Opening file </Users/tfr23/Documents/affytest/HuGeneMixRMAMetacore.root>
>> in <READ> mode...
>> Exporting data from tree <*> to file
>> </Users/tfr23/Documents/affytest/HuGeneMixRMAMetacore.txt>...
>> Reading entries from <HuGene-1_0-st-v1.ann> ...Finished
>> <57> of <57> records exported.
>>
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