HI All,
I am trying to run the standard procedures for a HuGene-1_0-st-v1 array.
Here is the code:
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setwd("<my work dir ...>");
library(aroma.affymetrix)
chipType <- "HuGene-1_0-st-v1"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
print(cdf)
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At this stage the program crashes (segmentation fault). This is the output:
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*** caught segfault ***
address 0xfffffffc, cause 'memory not mapped'
Traceback:
1: .Call("R_affx_get_cdf_file_header", filename, PACKAGE = "affxparser")
2: readCdfHeader(getPathname(this))
3: getHeader.AffymetrixCdfFile(this)
4: getHeader(this)
5: getChipType.AffymetrixCdfFile(this)
6: getChipType(this)
7: sprintf("Chip type: %s", getChipType(this))
8: as.character.AromaChipTypeAnnotationFile(x)
9: NextMethod("as.character", this, ...)
10: as.character.AffymetrixCdfFile(x)
11: as.character(x)
12: print(as.character(x))
13: print.Object(cdf)
14: print(cdf)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
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My working directory is according to the required folder structure.
Specifically it includes:
$ROOT/annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf
$ROOT/rawData/$PROJECT1/HuGene-1_0-st-v1/File1.CEL
The HuGene-1_0-st-v1,r3.cdf was downloaded from the aroma-project web
site: http://aroma-project.org/vignettes/GeneSTArrayAnalysis
I am using R version 2.15 (tried both R64 and R) on a Mac OSX 6.
Help!!!
Nir
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