Hi Setting aside the obvious problems with the NCBI ftp site at present..... I manually downloaded a series matrix file, GSE6198_series_matrix.txt.gz and I have two questions: Firstly, why am I getting these errors: > geo <- getGEO(file="GSE6198_series_matrix.txt.gz", GSEMatrix=TRUE) File stored at: C:\WINDOWS\TEMP\Rtmpjjh5g4/GPL1836.soft Error in validObject(.Object) : invalid class "ExpressionSet" object: featureNames differ between assayData and featureData In addition: Warning message: In download.file(myurl, destfile, mode = mode, quiet = TRUE) : downloaded length 2799566 != reported length 200 Secondly, is there a way to instruct getGEO not to download the GPL, but instead, to use a pre-downloaded GPL I have stored somewhere else? Thanks Mick [[alternative HTML version deleted]]