[BioC] xps rma() with HuGene-1_0-st-v1 on 64-bit architecture
Tim Rayner
tfrayner at gmail.com
Tue Feb 17 18:52:34 CET 2009
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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