On Thu, Dec 11, 2014 at 4:52 AM, Rishi Das Roy wrote:
> Hi
>
> Thanks for your reply. I can understand that I can identify alternative
> splicing through FIRMA more confidently. However I also want to identify
> differentially expressed genes. I have not find any documentation regarding
> this in
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 DChipSn
Try this instead:
csv <- AffymetrixNetAffxCsvFile$byChipType("CytoScanHD_Array",
pattern="_annot[.]csv")
I've updated http://aroma-project.org/setup/annotationData accordingly.
I'll try fix the bug forcing us to specifying 'pattern' this way.
Thanks for the report
/Henrik
On Mon, Dec 15, 2014
#x27;aroma.affymetrix'
Error: Failed to retrieve genome information for this chip type:
CytoScanHD_Array
>si <- getSnpInformation(cdf)
20141215 18:31:41|Defining DChipSnpInformation from chip type...
20141215 18:31:41| Chip type: CytoScanHD_Array
20141215 18:31:41| Version:
20141215 18:
I can reproduce this;
> csv <- AffymetrixNetAffxCsvFile$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
Addtional information.
The file structure is like this,
├── annotationData
│ └── chipTypes
│ └── CytoScanHD_Array
│ ├── CytoScanHD_Array.cdf
│ └── NetAffx
│ └── CytoScanHD_Array_annot.csv
└── rawData
└── dataset1
└── CytoScanHD_Array
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
