Dear all
I run into an error while setting up a CELset with my data. I've checked
the structure of the folder annotationData and rawData and this is as
instructed. My working directory contains the folders annotationData and
rawData which both have a folder "hjay" (my chiptype) containing the cdf
and CEL files respectively. My code is as follows:
library(aroma.affymetrix)
chipType<-"hjay"
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="r1,TC")
print(cdf)
# AffymetrixCdfFile:
# Path: annotationData/chipTypes/hjay
# Filename: hjay,r1,TC.cdf
# File size: 103.36 MiB (108385660 bytes)
# Chip type: hjay,r1,TC
# RAM: 0.00MB
# File format: v4 (binary; XDA)
# Dimension: 2558x2560
# Number of cells: 6548480
# Number of units: 33516
# Cells per unit: 195.38
# Number of QC units: 0
cs <- AffymetrixCelSet$byName("Data_Study1",cdf=cdf,verbose=TRUE);
#which runs into the following error
Exception: 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 'hjay' (without requiring any tags) and with filename extension 'cdf'.
(while trying './rawData/Data_Study1/hjay').
at #03. byName.AffymetrixCelSet(static, ...)
- byName.AffymetrixCelSet() is in environment 'aroma.affymetrix'
at #02. byName(static, ...)
- byName() is in environment 'R.filesets'
- originating from '<text>'
at #01. AffymetrixCelSet$byName("HTA_RASA", cdf = cdf, verbose = TRUE)
- AffymetrixCelSet$byName() is local of the calling function
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 'hjay'
(without requiring any tags) and with filename extension 'cdf'. (while
trying './rawData/HTA_RASA/hjay').
I created the cdf file myself. Is it possible that that I made a mistake
during this process that can already be detected by AffymetrixCelSet$byName?
Thank you for any help!
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