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I am having some difficulty with the goTools package. Specifically I am getting the error message Error in goidvect[test] : invalid subscript type 'list' First I load the GOTerms goAnnotation2 <- read.table("C:/Users/Kristi 2/Desktop/test.txt", sep="\t", header=TRUE, colClasses="character") Which looks like this GOTerm GO:0050517 GO:0050432 GO:0005515 GO:0003677 GO:0008270 GO:0030548 GO:0050517 GO:0050432 GO:0005515 GO:0051010 goAnnotation2 <- as.vector(unlist(goAnnotation2)) class(goAnnotation2)  "character" Count = ontoCompare(list(goAnnotation2), probeType="GO", method="TIDS") Starting ontoCompare... Error in goidvect[test] : invalid subscript type 'list' I found a similar error discussed August 4, 2011. The OP posted the code that they could not execute successfully on their machine, although the example they gave worked for me. I'm running Windows 7 box, core i7 processor with 8GB RAM, and I'm using R-Studio. Note, that the above list of GO terms isn't the actual list of GO terms I wish to include, it's just a random I am starting with to get my hands wet with goTools. I have some work to do yet to extract all the GO terms from our microarray annotation file which annoyingly included the textual descriptions for each GO term beside it (e.g. GO:0032422: purinE-rich negative regulatory element binding; GO:0003714: transcription corepressor activity; GO:0003700: transcription factor activity) Thanks, Brad -- output of sessionInfo(): R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale:  LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252  LC_NUMERIC=C LC_TIME=English_Canada.1252 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  goTools_1.28.0 GO.db_2.6.1 RSQLite_0.11.1 DBI_0.2-5  AnnotationDbi_1.16.19 Biobase_2.14.0 loaded via a namespace (and not attached):  IRanges_1.12.6 tools_2.14.1 -- Sent via the guest posting facility at bioconductor.org.