[BioC] xps rma() with HuGene-1_0-st-v1 on 64-bit architecture
cstrato
cstrato at aon.at
Tue Feb 17 20:05:42 CET 2009
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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