[BioC] error reading GSE file

Sean Davis 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)
> Parsing....
> 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'

Hi, Reema.

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.


More information about the Bioconductor mailing list