Hi, I think Jennifer and I got this fixed a few days ago. Hopefully the new version in the devl branch solves this problem. Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jennifer Lai Sent: 31 August 2005 15:28 To: bioconductor at stat.math.ethz.ch Subject: [BioC] affymetrix latin square 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 mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}