Hi, I'm using GEOquery 2.4.1 to read an NCBI GEO file ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4284/GSE4284_serie s_matrix.txt.gz but parseGEO throws an error. The switch argument evaluates to "0", which doesn't match alternative, so it tries to match on the last empty argument and fails. I don't know if this is related to the warnings; the file contains text such as manufacturer\xa1\xafs which may not parse correctly. Below is the output. Thanks for any advice, Gad > g <- getGEO(filename="GSE4284_series_matrix.txt") Error in switch(as.character(first.entity[1]), sample = { : argument is missing, with no default In addition: Warning messages: 1: In grep("^\\^(DATASET|SAMPLE|SERIES|PLATFORM|ANNOTATION)", line, : input string 1 is invalid in this locale 2: In grep("^\\^(DATASET|SAMPLE|SERIES|PLATFORM|ANNOTATION)", line, : input string 1 is invalid in this locale > debugger() Message: Error in switch(as.character(first.entity[1]), sample = { : argument is missing, with no default Available environments had calls: 1: getGEO(filename = "GSE4284_series_matrix.t 2: parseGEO(con, GSElimits) 3: switch(as.character(first.entity[1]), sample = { Enter an environment number, or 0 to exit Selection: 2 Browsing in the environment with call: parseGEO(con, GSElimits) Called from: debugger.look(ind) Browse[1]> as.character(first.entity[1]) [1] "0" > sessionInfo() R version 2.7.1 (2008-06-23) i486-pc-linux-gnu locale: LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GEOquery_2.4.1 RCurl_0.9-3 Biobase_2.0.1 -- Gad Abraham Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham