Question: GEOquery error when parsing Agilent annotation (?)
gravatar for Axel Klenk
8.2 years ago by
Axel Klenk920
Axel Klenk920 wrote:
Dear BioC list and esp. Sean, I'm trying to download GSE15197 using GEOquery and get the following error: > gse15197 <- getGEO(GEO = "GSE15197", destdir = ".", AnnotGPL = TRUE) Found 1 file(s) GSE15197_series_matrix.txt.gz trying URL ' ries_matrix.txt.gz' ftp data connection made, file length 6566671 bytes opened URL ================================================== downloaded 6.3 Mb File stored at: /tmp/RtmpDBAlMH/GPL6480.soft Error in `row.names<`(`*tmp*`, value = c("A_23_P100001", "A_23_P100011", : missing values in 'row.names' are not allowed > traceback() 7: stop("missing values in 'row.names' are not allowed") 6: `row.names<`(`*tmp*`, value = c("A_23_P100001", "A_23_P100011", "A_23_P100022", "A_23_P100056", "A_23_P100074", "A_23_P100092", [... lots of Agilent oligo IDs ...] "ETG10_13482", "ETG10_195139", "ETG10_234183", "ETG10_236652", "GE_BrightCorner", NA, "RC1", "RC10", "RC11", "RC12", "RC2", "RC3", "RC4", "RC5", "RC6", "RC7", "RC8", "RC9")) 5: `row.names<-`(`*tmp*`, value = c("A_23_P100001", "A_23_P100011", "A_23_P100022", "A_23_P100056", "A_23_P100074", "A_23_P100092", [... lots of Agilent oligo IDs ...] "ETG10_13482", "ETG10_195139", "ETG10_234183", "ETG10_236652", "GE_BrightCorner", NA, "RC1", "RC10", "RC11", "RC12", "RC2", "RC3", "RC4", "RC5", "RC6", "RC7", "RC8", "RC9")) 4: `rownames<-`(`*tmp*`, value = c("A_23_P100001", "A_23_P100011", "A_23_P100022", "A_23_P100056", "A_23_P100074", "A_23_P100092", [... lots of Agilent oligo IDs ...] "ETG10_13482", "ETG10_195139", "ETG10_234183", "ETG10_236652", "GE_BrightCorner", NA, "RC1", "RC10", "RC11", "RC12", "RC2", "RC3", "RC4", "RC5", "RC6", "RC7", "RC8", "RC9")) 3: parseGSEMatrix(file.path(tmp, b[i])) 2: getAndParseGSEMatrices(GEO) 1: getGEO(GEO = "GSE15197", destdir = ".", AnnotGPL = TRUE) which apparently occurs after successful download of the data files when trying to parse GPL6480 annotation (?) and according to the error message the NA near the end of the value list may be the culprit. Setting AnnotGPL to FALSE gives the same result. Since the identical procedure usually works, is there a problem with this particular data set or am I missing something? Thanks a lot in advance, - axel > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 [4] limma_3.4.0 sfsmisc_1.0-11 geneplotter_1.26.0 [7] lattice_0.18-8 annotate_1.26.0 AnnotationDbi_1.10.0 [10] Biobase_2.8.0 MASS_7.3-5 gmodels_2.15.0 [13] fortunes_1.3-7 loaded via a namespace (and not attached): [1] DBI_0.2-5 gdata_2.8.0 grid_2.11.0 gtools_2.6.2 [5] RColorBrewer_1.0-2 RSQLite_0.9-0 xtable_1.5-6 Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at
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