Question: Problem in downloading GSE
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gravatar for Harpreet Saini
10.6 years ago by
United Kingdom
Harpreet Saini30 wrote:
Hi, I am getting problem in downloading a particular GSE matrix file (GSE1074) as an expression set by turning the GSEMatrix 'true' as following: gseid<-"GSE1074" GEOgse<-getGEO(gseid,GSEMatrix=TRUE) The GSE1074 has two platforms, GPL1261 and GPL560. I am able to download the GSE1074_GPL1261_series_matrix.txt, but getting the following error for GSE1074_GPL560_series_matrix.txt file. trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE1074/G SE1074-GPL560_series_matrix.txt.gz' ftp data connection made, file length 69494 bytes opened URL ================================================== downloaded 67 Kb Error in read.table(con, sep = "\t", header = FALSE, nrows = i) : incomplete final line found by readTableHeader on GSE1074- GPL560_series_matrix.txt.gz The sessionInfo() is R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tools stats graphics grDevices datasets utils methods [8] base other attached packages: [1] biomaRt_1.16.0 limma_2.16.5 GEOmetadb_1.2.1 RSQLite_0.7-1 [5] DBI_0.2-4 GEOquery_2.6.0 RCurl_0.94-1 Biobase_2.2.2 [9] R.utils_1.1.1 R.oo_1.4.6 R.methodsS3_1.0.3 loaded via a namespace (and not attached): [1] XML_2.3-0 Any help? Thanks Harpreet Harpreet Kaur Saini Enright Group EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: +44-(0) 1223-492676 [[alternative HTML version deleted]]
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