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.afymetrix package. Maybe I was using
wrong way.
Any comments are appreciated.
> cdf <- AffymetrixCdfFile$byChipType('CytoScanHD_Array');
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/CytoScanHD_Array
Filename: CytoScanHD_Array.cdf
File size: 612.27 MB (642007896 bytes)
Chip type: CytoScanHD_Array
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 2822125
Cells per unit: 2.44
Number of QC units: 4
>gi <- getGenomeInformation(cdf)
[2014-12-15 18:28:32] Exception: Failed to retrieve genome information for
this chip type: CytoScanHD_Array
at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
- getGenomeInformation.AffymetrixCdfFile() is in environment
'aroma.affymetrix'
at #01. getGenomeInformation(cdf)
- getGenomeInformation() is in environment 'aroma.affymetrix'
Error: Failed to retrieve genome information for this chip type:
CytoScanHD_Array
>si <- getSnpInformation(cdf)
20141215 18:31:41|Defining DChipSnpInformation from chip type...
20141215 18:31:41| Chip type: CytoScanHD_Array
20141215 18:31:41| Version:
20141215 18:31:41| Located pathname:
20141215 18:31:41|Defining DChipSnpInformation from chip type...done
[2014-12-15 18:31:41] Exception: Failed to retrieve SNP information for
this chip type: CytoScanHD_Array
at #02. getSnpInformation.AffymetrixCdfFile(cdf)
- getSnpInformation.AffymetrixCdfFile() is in environment
'aroma.affymetrix'
at #01. getSnpInformation(cdf)
- getSnpInformation() is in environment 'aroma.affymetrix'
Error: Failed to retrieve SNP information for this chip type:
CytoScanHD_Array
>acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
[2014-12-15 18:31:50] Exception: Failed to create AromaCellSequenceFile
object. Could not locate an annotation data file for chip type
'CytoScanHD_Array' (without requiring any tags) and with filename extension
'acs'.
at #03. byChipType.AromaMicroarrayTabularBinaryFile(static, ...)
- byChipType.AromaMicroarrayTabularBinaryFile() is in environment
'aroma.core'
at #02. byChipType(static, ...)
- byChipType() is in environment 'aroma.core'
- originating from '<text>'
at #01. AromaCellSequenceFile$byChipType(getChipType(cdf, fullname =
FALSE))
- AromaCellSequenceFile$byChipType() is local of the calling
function
Error: Failed to create AromaCellSequenceFile object. Could not locate an
annotation data file for chip type 'CytoScanHD_Array' (without requiring
any tags) and with filename extension 'acs'.
On Monday, December 15, 2014 6:27:51 PM UTC+2, Henrik Bengtsson wrote:
>
> I can reproduce this;
>
> > csv <- AffymetrixNetAffxCsvFile$byChipType(chipType)
> Error in grep(pattern, basename(files0)) : invalid 'pattern' argument
>
> I'll investigate.
>
> /Henrik
>
> On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu <chengyu...@gmail.com
> <javascript:>> wrote:
> > Hi,
> >
> > I am trying to read annotation file of CytoScanHD_Array, but somehow it
> > could not locate it.
> >
> > I followed the tutorial in the web
> > http://aroma-project.org/setup/annotationData/. I am using NetAffx
> > Annotation Files (I could not find CDF file) .
> > I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/ and
> put
> > annotation file CytoScanHD_Array_annot.csv there.
> >
> > I ran AffymetrixNetAffxCsvFile$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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