I attempted to use the script posted on the site to convert the
pd.hugene.1.0.st.v1 package to a CDF file but it appears not to be
working. The resulting cdf file has too many units and
aroma.affymetrix will not work with it beyond naming the CDF. Are you
aware of any issues?
source("http://bioinf.wehi.edu.au/folders/mrobinson/aroma/PdInfo2Cdf.R";)
PdInfo2Cdf("pd.hugene.1.0.st.v1", "A1_Affy.CEL", overwrite=TRUE)
I renamed the resulting binary cdf file and moved it to the appropriate
aroma.affymetrix directory.
setwd("P:\\ANNOTATION\\aromaAffymetrix")
library(aroma.affymetrix)
chipType <- "HuGene-1_0-st-v1"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r4")
print(cdf)
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuGene-1_0-st-v1
Filename: HuGene-1_0-st-v1,r4.cdf
Filesize: 51.94MB
Chip type: HuGene-1_0-st-v1,r4
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1050x1050
Number of cells: 1102500
Number of units: 253002
Cells per unit: 4.36
Number of QC units: 0
--
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.
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