problem with CDF file

[Zsuzsa]

Hello Henrik,

I am trying to use the the aroma.affymetrix package to check the
quality of some mouse GeneST arrays. I got stuck with the cdf file.
I downloaded the unsupported cdf file from Affymetrix, placed it in
annotationData/chipTypes/MoGene-1_0-st-v1 folder and the run the
following commands:
library(affxparser)
convertCdf(filename = "C:/Program Files/R/R-2.9.0/library/
aroma.affymetrix/annotationData/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-
st-v1.r3.cdf",
outFilename = "C:/Program Files/R/R-2.9.0/library/aroma.affymetrix/
annotationData/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,r3.cdf")

library(aroma.affymetrix)
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
chipType <- "MoGene-1_0-st-v1"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")

The problem is I am getting the following error message:
Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = "r3")` =
<environment>, :

[2010-07-12 12:42:56] Exception: Could not locate a file for this chip
type: MoGene-1_0-st-v1,r3
at throw(Exception(...))
at throw.default("Could not locate a file for this chip type: ",
paste(c(chipType, tags), collapse = ","))
at throw("Could not locate a file for this chip type: ",
paste(c(chipType, tags), collapse = ","))
at method(static, ...)
at AffymetrixCdfFile$byChipType(chipType, tags = "r3")

I think the function is looking for the file someplace else, but I
don't know where. Would you be able to help me out on this.

Thank you.
Zsuzsa

[Henrik Bengtsson]

Hi,

before continuing, do you have the latest version of aroma.affymetrix
(v1.6.0) installed, e.g. what does

library("aroma.affymetrix");
print(sessionInfo());

report? You probably also want to update to R v2.11.1 (R v2.9.0 is rather old).

Second, the annoationData/ directory should be located in your working
directory, i.e.

print(getwd());

I doubt that 'C:/Program Files/R/R-2.9.0/library/aroma.affymetrix/' is
your working directory. See thread 'Could not locate a file for this
chip type (Was: ...)' from August 27, 2009

http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/c18f714638a6eb24/9b34427b16128ef3

for more troubleshooting tricks.

/Henrik

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