> library(simpleaffy) > x <- read.affy("covdesc") > x.mas5 <- call.exprs(x,"mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ......done. scaling to a TGT of 100 ... Scale factor for: bot0343.CEL 1.19431517356046 Scale factor for: bot0344.CEL 1.25599200206275 Scale factor for: bot0345.CEL 1.72226407855678 Scale factor for: bot0340.CEL 1.45162850888082 Scale factor for: bot0341.CEL 0.960621730495837 Scale factor for: bot0342.CEL 1.34367816094756 > qc <- qc(x,x.mas5) Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: poplarcdf Note that in the sessionInfo() output below I have simpleaffy 2.4.2 which was installed by biocLite. Afterwards I manually upgraded simpleaffy to 2.6.0, which had no effect. Any suggestions? > cdfName(raw.data) [1] "Poplar" > sessionInfo() Version 2.3.1 (2006-06-01) i486-pc-linux-gnu attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: poplarcdf simpleaffy genefilter survival affy affyio Biobase "1.12.0" "2.4.2" "1.10.1" "2.26" "1.10.0" "1.0.0" "1.10.1" after upgrading simpleaffy: > sessionInfo() Version 2.3.1 (2006-06-01) i486-pc-linux-gnu attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: poplarcdf simpleaffy genefilter survival affy affyio Biobase "1.12.0" "2.6.0" "1.10.1" "2.26" "1.10.0" "1.0.0" "1.10.1"