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]]

