Try this instead:
csv <- AffymetrixNetAffxCsvFile$byChipType("CytoScanHD_Array",
pattern="_annot[.]csv")
I've updated http://aroma-project.org/setup/annotationData accordingly.
I'll try fix the bug forcing us to specifying 'pattern' this way.
Thanks for the report
/Henrik
On Mon, Dec 15, 2014 at 8:27 AM, Henrik Bengtsson <h...@biostat.ucsf.edu> wrote:
> I can reproduce this;
>
>> csv <- AffymetrixNetAffxCsvFile$byChipType(chipType)
> Error in grep(pattern, basename(files0)) : invalid 'pattern' argument
>
> I'll investigate.
>
> /Henrik
>
> On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu <chengyu.liu...@gmail.com> wrote:
>> Hi,
>>
>> I am trying to read annotation file of CytoScanHD_Array, but somehow it
>> could not locate it.
>>
>> I followed the tutorial in the web
>> http://aroma-project.org/setup/annotationData/. I am using NetAffx
>> Annotation Files (I could not find CDF file) .
>> I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/ and put
>> annotation file CytoScanHD_Array_annot.csv there.
>>
>> I ran AffymetrixNetAffxCsvFile$byChipType("CytoScanHD_Array") at parent
>> directory of annotationData.
>>
>> It gave error "Error in grep(pattern, basename(files0)) : invalid 'pattern'
>> argument"
>>
>> Does anyone know what was wrong ?
>>
>> Br,
>> C.Y
>>
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