Hi Bioconductor users, I encounter a problem in library GEOquery, I downloaded soft format gene expression profile from GEO database. whenever I run below lines, there appears a warning message though already read in the soft file. > setwd("C:\\work\\microarray\\Implementation") > GSE781<- getGEO(filename = "GSE781_family.soft.gz") There were 50 or more warnings (use warnings() to see the first 50) Warning messages: 1: In readLines(con, 1) : seek on a gzfile connection returned an internal error 2: In readLines(con, 1) : seek on a gzfile connection returned an internal error 3: In readLines(con, 1) : seek on a gzfile connection returned an internal error 4: In readLines(con, 1) : seek on a gzfile connection returned an internal error 5: In readLines(con, 1) : seek on a gzfile connection returned an internal error 6: In readLines(con, 1) : seek on a gzfile connection returned an internal error > sessionInfo() R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] splines stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] annotate_1.30.0 affydata_1.11.11 affy_1.30.0 [4] flexmix_2.3-5 multcomp_1.2-7 survival_2.36-9 [7] mvtnorm_0.9-9991 modeltools_0.2-17 lattice_0.19-30 [10] bioDist_1.24.1 KernSmooth_2.23-6 genefilter_1.34.0 [13] hgu133a.db_2.5.0 org.Hs.eg.db_2.5.0 RSQLite_0.9-4 [16] DBI_0.2-5 AnnotationDbi_1.14.1 reshape_0.8.4 [19] plyr_1.6 GEOquery_2.19.3 Biobase_2.12.2 loaded via a namespace (and not attached): [1] affyio_1.20.0 grid_2.13.1 preprocessCore_1.14.0 [4] RCurl_1.6-7.1 tools_2.13.1 XML_3.4-2.2 [7] xtable_1.5-6 Anyone knows how to deal with the above problems, thanks a lot in advance! -- Best Regards, Zhe Liu [[alternative HTML version deleted]]