Hi, I am trying to speed up my mas5 processing by using justMAS on my affybatch. My AffyBatch is made of 8 chips and the cdf for these chips is hgu133a. I have tested justMAS by running it several times on this affybatch and I am obtaining different expression measure results even though I am doing the exact same command. My affybatch is called 'F' and an array of geneNames is called 'gn', and I type: > j<-justMAS(F) > j at exprs[gn=="1007_s_at"] 1007_s_at <na> <na> <na> <na> <na> <na> <na> 6.603113 6.171309 6.399581 6.171309 6.171309 6.171309 6.171309 6.036457 > i<-justMAS(F) > i at exprs[gn=="1007_s_at"] 1007_s_at <na> <na> <na> <na> <na> <na> <na> 6.603113 NaN 6.171309 5.482231 6.171309 5.438713 5.387300 7.311159 Does anybody know why I am getting this discrepancy? -Eitan

I think I replied to this already? Hi, I've just had a look at this... I think you probably want a comma after "1007_s_at"; exprs is a 2D matrix: Try: exprs(j)[gn=="1007_s_at",] ^ | Note the comma (exprs(j) should give you the same things as j at exprs) I get the same results when I call justMAS more than once (trying to duplicate your example). If you're still having problems let me know - but with more details (what version of R, what version of simpleaffy, what machine you're running it on etc...). Hope that helps, Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Eitan Halper-Stromberg Sent: 24 June 2005 20:51 To: bioconductor at stat.math.ethz.ch Subject: [BioC] justMAS reliability Hi, I am trying to speed up my mas5 processing by using justMAS on my affybatch. My AffyBatch is made of 8 chips and the cdf for these chips is hgu133a. I have tested justMAS by running it several times on this affybatch and I am obtaining different expression measure results even though I am doing the exact same command. My affybatch is called 'F' and an array of geneNames is called 'gn', and I type: > j<-justMAS(F) > j at exprs[gn=="1007_s_at"] 1007_s_at <na> <na> <na> <na> <na> <na> <na> 6.603113 6.171309 6.399581 6.171309 6.171309 6.171309 6.171309 6.036457 > i<-justMAS(F) > i at exprs[gn=="1007_s_at"] 1007_s_at <na> <na> <na> <na> <na> <na> <na> 6.603113 NaN 6.171309 5.482231 6.171309 5.438713 5.387300 7.311159 Does anybody know why I am getting this discrepancy? -Eitan _______________________________________________ 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}}