[BioC] error reading GSE file
sdavis2 at mail.nih.gov
Tue Jul 26 14:39:42 CEST 2011
On Tue, Jul 26, 2011 at 6:38 AM, Reema Singh <reema28sep at gmail.com> wrote:
> Dear all
> I am trying to read a GSE file in R using GEOquery package but i am getting
> following error.Kindly tell me why i am getting this error. I have tried to
> find out on google. But no luck...
> u <- getGEO(filename="GSE1106_family.soft",GSEMatrix=TRUE)
> Found 22 entities...
> GPL199 (1 of 22 entities)
> GSM18235 (2 of 22 entities)
> GSM18236 (3 of 22 entities)
> Error in substr(x, start = matches + patlen, stop = 1e+07) :
> invalid multibyte string at '<92>s pre'
This is caused by an invalid character in the data from NCBI. I have
contacted them to fix the problem. In the meantime, you can try:
u = getGEO('GSE1106')
This will grab the GSEMatrix file which is apparently unaffected.
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