Hi Sean, Thanks a bunch! Regards, Avoks On Fri, Oct 14, 2011 at 11:03 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Fri, Oct 14, 2011 at 4:40 AM, Ovokeraye Achinike-Oduaran > <ovokeraye at="" gmail.com=""> wrote: >> >> Hi all, >> >> In trying to create a contrast matrix of interest, I thought it would >> be easier to assign one-word names to the different disease states. I >> seem to have gotten it to work for the GDS3715 data set that happens >> to be a 3x2 factorial experiment, I think. But for the seemingly less >> complex GDS3665, I ?can't seem to get it right. It keeps giving me >> these errors(below). Any ideas as to what I could possibly be doing >> wrong? Any help will be greatly appreciated. >> >> Thanks. >> >> -Avoks >> >> >> >> >gds3665dat = getGEO('GDS3665',destdir=".") >> >gds3665eset = GDS2eSet(gds3665dat, do.log2=TRUE) >> > groups= pData(gds3665eset)$disease.state >> > groups >> ?[1] diabetes diabetes diabetes diabetes diabetes control ?control ?control >> ?[9] control ?control >> Levels: control diabetes >> >> > groups[groups=="control"]="Control" >> Warning message: >> In `[<-.factor`(`*tmp*`, groups == "control", value = "Control") : >> ?invalid factor level, NAs generated >> > groups[groups=="diabetes"]="T2D" >> Warning message: >> In `[<-.factor`(`*tmp*`, groups == "diabetes", value = "T2D") : >> ?invalid factor level, NAs generated > > Hi, Avoks. > > "groups" above is a factor, not a character vector. ?They look the > same, but they are different. ?In the case below, you used paste() > which creates a character vector; hence, the behavior is different. > If you convert to a character vector first, things will work as > expected. > > groups <- as.character(groups) > > Alternatively, you can use levels() to change the levels for the > factor. ?Check the help for levels, relevel, factor, and as.character > for details. > > Sean > > >> > groups >> ?[1] <na> <na> <na> <na> <na> <na> <na> <na> <na> <na> >> Levels: control diabetes >> >> This, however, works just fine. >> >> gds3715dat = getGEO('GDS3715',destdir=".") >> gds3715eset = GDS2eSet(gds3715dat, do.log2=TRUE) >> groups = paste(pData(gds3715eset)$disease.state, >> pData(gds3715eset)$agent, sep =".") >> groups[groups=="insulin sensitive.untreated"]= "IS.U" >> groups[groups=="insulin resistant.untreated"]= "IR.U" >> groups[groups=="diabetic.untreated"]= "T2D.U" >> groups[groups=="insulin sensitive.insulin"]= "IS.T" >> groups[groups=="insulin resistant.insulin"]= "IR.T" >> groups[groups=="diabetic.insulin"]= "T2D.T" >> > sessionInfo() >> R version 2.13.2 (2011-09-30) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_xxx ?LC_CTYPE=English_xxx >> [3] LC_MONETARY=English_xxx LC_NUMERIC=C >> [5] LC_TIME=English_xxx >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] XML_3.4-2.2 ? ? RCurl_1.6-10.1 ?bitops_1.0-4.1 ?puma_2.4.0 >> [5] mclust_3.4.10 ? affy_1.30.0 ? ? limma_3.8.3 ? ? GEOquery_2.19.4 >> [9] Biobase_2.12.2 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.20.0 ? ? ? ? preprocessCore_1.14.0 tools_2.13.2 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >