Hi,
I am using a Custom cdf file *HTA-2_0,Transcript,binary.cdf* in aroma.
affymetrix to analyse HTA-2_0 chip . I am using the following commands to
set up CDF and CEL files.
>chipType <- "HTA-2_0"
>cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Transcript,binary")
>print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/HTA-2_0
Filename: HTA-2_0,Transcript,binary.cdf
File size: 7.55 MB (7921066 bytes)
Chip type: HTA-2_0,Transcript,binary
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 18490
Cells per unit: 354.44
Number of QC units: 0
>cs<-AffymetrixCelSet$byName("Krzy",cdf=cdf,verbose=verbose)
However I am unable to read the CEL files as it gives me the following
error:
Error: Failed to setup a data set for any of 1 data directories located.
The following reasons were reported: (1) Failed to create AffymetrixCdfFile
object. Could not locate an annotation data file for chip type 'HTA-2_0'
(without requiring any tags) and with filename extension 'cdf'. (while
trying './rawData/Krzy/HTA-2_0').
My directory structure is:
annotationData< chipTypes<HTA-2_0<HTA-2_0,Transcript,binary.cdf
rawData<Krzy<HTA-2_0<K15P.CEL
Please can someone help me understanding what I am doing wrong. I have used
aroma.affymetrix for exon arrays and I never came across this issue. Is it
something to do with the CDF file?
Kind Regards,
Sanjana
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
