Hi,
I have built R (current development version) and BioConductor 1.7
with portland group compiler on a AMD Opteron.
When I ran qc assessment on Affymetrix latin square data set, I got the
following output,
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
Loading required package: reposTools
Welcome to 'simpleaffy' V 2.1.3
Produced by The Paterson Institute for Cancer Research
and funded by CANCER RESEARCH UK.
http://bioinformatics.picr.man.ac.uk/simpleaffy
mailto: microarray at picr.man.ac.uk
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
.........................done.
scaling to a TGT of 100 ...
Scale factor for: 0203_YH10_H_MCF7_r1.CEL 0.291660289301555
Scale factor for: 0203_YH11_H_MCF10A_r1.CEL 0.42025300545212
Scale factor for: 0203_YH12_H_a100MCF7_r1.CEL 0.287589038746987
Scale factor for: 0203_YH13_H_a100MCF10A_r1.CEL 0.451200408584071
Scale factor for: 0203_YH14_H_a10MCF7_r1.CEL 0.385462078301135
Scale factor for: 0203_YH15_H_a100MCF7_r2.CEL 0.284974495993646
Scale factor for: 0203_YH16_H_a100MCF7_r3.CEL 0.376484877281483
Scale factor for: 0203_YH17_H_a100MCF10A_r2.CEL 0.374087365857816
Scale factor for: 0203_YH18_H_a100MCF10A_r3.CEL 0.487207458237659
Scale factor for: 0203_YH19_H_a10MCF7_r2.CEL 0.413217979158927
Scale factor for: 0203_YH20_H_a10MCF7_r3.CEL 0.482703032325383
Scale factor for: 0203_YH21_H_a10MCF10A_r1.CEL 0.945369712044904
Scale factor for: 0203_YH22_H_a10MCF10A_r2.CEL 1.96143996386198
Scale factor for: 0203_YH23_H_a10MCF10A_r3_rescan.CEL 0.841535915879218
Scale factor for: 0203_YH24_H_MCF7_r2.CEL 0.347795838770919
Scale factor for: 0203_YH25_H_MCF7_r3.CEL 0.318539156900791
Scale factor for: 0203_YH26_H_MCF10A_r2.CEL 0.578922233010316
Scale factor for: 0203_YH27_H_MCF10A_r3.CEL 0.394833650209601
Scale factor for: 0403_YH34_H_a10MCF10A_r4.CEL 1.06804698986081
Scale factor for: 0403_YH35_H_a1MCF7_r1_2.CEL 3.5923019165673
Scale factor for: 0403_YH36_H_a1MCF7_r2.CEL 3.16130786066591
Scale factor for: 0403_YH37_H_a1MCF7_r3_2.CEL 2.01330391697437
Scale factor for: 0403_YH38_H_a1MCF10A_r1.CEL 0.923881702153984
Scale factor for: 0403_YH39_H_a1MCF10A_r2_2.CEL 2.29265379531566
Scale factor for: 0403_YH40_H_a1MCF10A_r3.CEL 4.02474777803345
Getting probe level data...
Computing p-values
Doing PMA Calls
TEST 1 : time Elapsed = 0 1 20
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
.........Error in FUN(X[[9]], ...) : Expecting 22283 unique probesets,
found 22284
Can anyone advise me on how to fix this problem? I was able to run the
same data set with gcc-compiled R2.1.1 and BioConductor 1.6 successfully.
Here is the code that I ran, if it helps to diagnose the problems.
library(simpleaffy);
library(affy);
ampli.data <- ReadAffy()
# normalize the data using call.exprs and mas5
ampli.eset <- call.exprs(ampli.data, "mas5")
# see what data is stored in ampli.eset at description@preprocssing
names(ampli.eset at description@preprocessing)
# acess each piece of information within
ampli.eset at description@preprocessing scale factors
ampli.eset at description@preprocessing$sfs
# filenames so that the scale factors can be related to their chips
ampli.eset at description@preprocessing$filenames
# tgt is the target intensity each chip was scaled to
ampli.eset at description@preprocessing$tgt
# which version of the affy package was used
ampli.eset at description@preprocessing$affyversion
qc.data <- qc(ampli.data, ampli.eset);
slotNames(qc.data);
# scale.factors contains a list of scale factors applied to each chip;
qc.data at scale.factors
# target is the target intensity that each chip was scaled to
qc.data at target
# percent.present is a list of the percentage of probesets called
present on each chip;
qc.data at percent.present
# average.background, minimum.background, maximum.background are all
lists detailing
# the average, minimum and maximum background for each chip;
qc.data at average.background
# spikes is a matrix containing normalized values for each of the spike
controls
colnames(qc.data at spikes)
Thanks,
Jennifer
Bioconductor and R-devel
2 messages · Jennifer Lai, Seth Falcon
Hi Jennifer, I'm moving this over to the bioconductor mail list since we are discussing Bioconductor packages, that would be the best place for the discussion at this point. Please subscribe and reply there. A couple quick comments: 1. You do realize BioC 1.7 is the current devel version, right? 2. After you see the error, try traceback() to get a better idea of where things are going wrong. Then you can use debug(someFunc) to debug in the place where the error occurs. I'm sure the package maintainers will be most receptive to any bug fixes. Best, + seth
On 31 Aug 2005, lai at lindaspaces.com wrote:
Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: reposTools Welcome to 'simpleaffy' V 2.1.3 Produced by The Paterson Institute for Cancer Research and funded by CANCER RESEARCH UK. http://bioinformatics.picr.man.ac.uk/simpleaffy mailto: microarray at picr.man.ac.uk Background correcting Retrieving data from AffyBatch...done. Computing expression calls... .........................done. scaling to a TGT of 100 ... Scale factor for: 0203_YH10_H_MCF7_r1.CEL 0.291660289301555 Scale factor for: 0203_YH11_H_MCF10A_r1.CEL 0.42025300545212 Scale factor for: 0203_YH12_H_a100MCF7_r1.CEL 0.287589038746987 Scale factor for: 0203_YH13_H_a100MCF10A_r1.CEL 0.451200408584071 Scale factor for: 0203_YH14_H_a10MCF7_r1.CEL 0.385462078301135 Scale factor for: 0203_YH15_H_a100MCF7_r2.CEL 0.284974495993646 Scale factor for: 0203_YH16_H_a100MCF7_r3.CEL 0.376484877281483 Scale factor for: 0203_YH17_H_a100MCF10A_r2.CEL 0.374087365857816 Scale factor for: 0203_YH18_H_a100MCF10A_r3.CEL 0.487207458237659 Scale factor for: 0203_YH19_H_a10MCF7_r2.CEL 0.413217979158927 Scale factor for: 0203_YH20_H_a10MCF7_r3.CEL 0.482703032325383 Scale factor for: 0203_YH21_H_a10MCF10A_r1.CEL 0.945369712044904 Scale factor for: 0203_YH22_H_a10MCF10A_r2.CEL 1.96143996386198 Scale factor for: 0203_YH23_H_a10MCF10A_r3_rescan.CEL 0.841535915879218 Scale factor for: 0203_YH24_H_MCF7_r2.CEL 0.347795838770919 Scale factor for: 0203_YH25_H_MCF7_r3.CEL 0.318539156900791 Scale factor for: 0203_YH26_H_MCF10A_r2.CEL 0.578922233010316 Scale factor for: 0203_YH27_H_MCF10A_r3.CEL 0.394833650209601 Scale factor for: 0403_YH34_H_a10MCF10A_r4.CEL 1.06804698986081 Scale factor for: 0403_YH35_H_a1MCF7_r1_2.CEL 3.5923019165673 Scale factor for: 0403_YH36_H_a1MCF7_r2.CEL 3.16130786066591 Scale factor for: 0403_YH37_H_a1MCF7_r3_2.CEL 2.01330391697437 Scale factor for: 0403_YH38_H_a1MCF10A_r1.CEL 0.923881702153984 Scale factor for: 0403_YH39_H_a1MCF10A_r2_2.CEL 2.29265379531566 Scale factor for: 0403_YH40_H_a1MCF10A_r3.CEL 4.02474777803345 Getting probe level data... Computing p-values Doing PMA Calls TEST 1 : time Elapsed = 0 1 20 Background correcting Retrieving data from AffyBatch...done. Computing expression calls... .........Error in FUN(X[[9]], ...) : Expecting 22283 unique probesets, found 22284 Can anyone advise me on how to fix this problem? I was able to run the same data set with gcc-compiled R2.1.1 and BioConductor 1.6 successfully. Here is the code that I ran, if it helps to diagnose the problems. library(simpleaffy); library(affy); ampli.data <- ReadAffy() # normalize the data using call.exprs and mas5 ampli.eset <- call.exprs(ampli.data, "mas5") # see what data is stored in ampli.eset at description@preprocssing names(ampli.eset at description@preprocessing) # acess each piece of information within ampli.eset at description@preprocessing scale factors ampli.eset at description@preprocessing$sfs # filenames so that the scale factors can be related to their chips ampli.eset at description@preprocessing$filenames # tgt is the target intensity each chip was scaled to ampli.eset at description@preprocessing$tgt # which version of the affy package was used ampli.eset at description@preprocessing$affyversion qc.data <- qc(ampli.data, ampli.eset); slotNames(qc.data); # scale.factors contains a list of scale factors applied to each # chip; qc.data at scale.factors # target is the target intensity that each chip was scaled to qc.data at target # percent.present is a list of the percentage of probesets called present on each chip; qc.data at percent.present # average.background, minimum.background, maximum.background are all lists detailing # the average, minimum and maximum background for each chip; qc.data at average.background # spikes is a matrix containing normalized values for each of the # spike controls colnames(qc.data at spikes) Thanks, Jennifer
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