On Mon, Oct 11, 2010 at 2:45 PM, Xiangqian Guo <xqguo@stanford.edu> wrote: > Dear Sean, > > I want to use GEOquery to download a GSE data from NCBI, but I tried > several times, Finally I failed, could you help me to figure it out ? > > Below is orders I have used: > > gselms <- getGEO("GSE17555",destdir=".",GSEMatrix = TRUE) > Found 6 file(s) > GSE17555-GPL8996_series_matrix.txt.gz > trying URL ' > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE17555/GSE17555-G PL8996_series_matrix.txt.gz > ' > ftp data connection made, file length 2798480 bytes > opened URL > downloaded 2.7 Mb > ………… > > File stored at: > C:\Users\XIANGQ~1\AppData\Local\Temp\RtmpkF6REV/GPL9000.soft > GSE17555-GPL9001_series_matrix.txt.gz > trying URL ' > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE17555/GSE17555-G PL9001_series_matrix.txt.gz > ' > ftp data connection made, file length 189222 bytes > opened URL > downloaded 184 Kb > > Error in names(x) <- value : > 'names' attribute [47] must be the same length as the vector [1] > In addition: Warning message: > closing unused connection 3 > (C:\Users\XIANGQ~1\AppData\Local\Temp\RtmpkF6REV/GSE17555-GPL9001_se ries_matrix.txt.gz) > > Thanks, Xiangqian, for the report. This is a bug in handling GSE Matrix files with only one sample. I believe the bug has been fixed at this point, but I think that the fix will likely not make it to the repository before the new version of bioconductor is released. You can either wait for that (next week) or download the beta version of R (2.12) and install GEOquery in a couple of days. Sean [[alternative HTML version deleted]]