On Jan 7, 2015 3:43 AM, "Chengyu Liu" wrote:
>
> Thanks，it is working now. I am sorry for the late reply. I was on
holidays and just back.
> About ACS, UGP and UFL, are they necessary for the copy number calls?
Yes.
Henrik
>
> Br,
>
>
> On Monday, December 15, 2014 8:25:17 PM UTC+2, Henrik Beng
Thanks，it is working now. I am sorry for the late reply. I was on holidays
and just back.
About ACS, UGP and UFL, are they necessary for the copy number calls?
Br,
On Monday, December 15, 2014 8:25:17 PM UTC+2, Henrik Bengtsson wrote:
>
> On Mon, Dec 15, 2014 at 8:38 AM, Chengyu Liu > wrote:
On Mon, Dec 15, 2014 at 8:38 AM, Chengyu Liu wrote:
> Thanks.
>
> I tried to bypass the NetAffx issue. I downloaded the cdf file from aroma
> (http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/)
> and Affymetrix website.
> Annotation file can be located, but following fun
Try this instead:
csv <- AffymetrixNetAffxCsvFile$byChipType("CytoScanHD_Array",
pattern="_annot[.]csv")
I've updated http://aroma-project.org/setup/annotationData accordingly.
I'll try fix the bug forcing us to specifying 'pattern' this way.
Thanks for the report
/Henrik
On Mon, Dec 15, 2014
Thanks.
I tried to bypass the NetAffx issue. I downloaded the cdf file from aroma
(http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/)
and Affymetrix website.
Annotation file can be located, but following functions does not work. It
was my first time to deal with aroma
I can reproduce this;
> csv <- AffymetrixNetAffxCsvFile$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 wrote:
> Hi,
>
> I am trying to read annotation file of CytoScanHD_Array, bu
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/CytoSc
