Error while setting up AffymetrixCelSet

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Marijke VAN MOERBEKE

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Aug 1, 2016, 12:27:06 PM8/1/16
to aroma.affymetrix
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!


Henrik Bengtsson

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Aug 7, 2016, 6:39:18 AM8/7/16
to aroma-affymetrix
Hmm... this looks weird but as usual, there's probably a simple
explanation to it. Yes, it could possibly be that the CDF is
incompatible with the CEL files, but in that case I'd expect an
informative error message explaining why.

In a fresh R session, what does the following output?

library("aroma.affymetrix")
cdf <- AffymetrixCdfFile$byChipType("hjay", tags="r1,TC")
cs <- AffymetrixCelSet$byName("Data_Study1", cdf=cdf, verbose=-100)

The output is quite long, but it'll help me/you troubleshoot.

Also, what's the output of sessionInfo() after the above?

/Henrik
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