[BioC] error reading GSE file

[Sean Davis]

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)
>> 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.

One has to love the GEO staff.  They've already fixed the problem.
Thanks for the report, Reema.

Sean

> In the meantime, you can try:
>
> u = getGEO('GSE1106')
>
> This will grab the GSEMatrix file which is apparently unaffected.
>
> Sean
>