[BioC] error reading GSE file
sdavis2 at mail.nih.gov
Tue Jul 26 16:16:19 CEST 2011
On Tue, Jul 26, 2011 at 8:39 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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'
> Hi, Reema.
> This is caused by an invalid character in the data from NCBI. I have
> contacted them to fix the problem.
One has to love the GEO staff. They've already fixed the problem.
Thanks for the report, Reema.
> In the meantime, you can try:
> u = getGEO('GSE1106')
> This will grab the GSEMatrix file which is apparently unaffected.
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