Hi, I have been trying to read the CDF files for the HuGene-1_0-st-v1
array with aroma.affymetrix and it has been very confuse for me.
I have the correct CDF files from the aroma page.
The CDF files are in the path: "/Library/Frameworks/R.framework/
Versions/2.11/Resources/library/aroma.affymetrix/annotationData/
chipTypes/HuGene-1_0-st-v1".
My working directory is: annotationData
but I still have this error:
#####################
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = "r3")` =
<environment>, :
[2010-09-27 06:14:53] Exception: Could not locate a file for this chip
type: HuGene-1_0-st-v1,r3
at throw(Exception(...))
at throw.default("Could not locate a file for this chip type: ", pa
at throw("Could not locate a file for this chip type: ", paste(c(ch
at method(static, ...)
at AffymetrixCdfFile$byChipType(chipType, tags = "r3")
##################
Also, if I look for the cdf path file in R, it returns NULL
>pathname <- "annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf"
> cdf <- AffymetrixCdfFile(pathname)
Error in list(`AffymetrixCdfFile(pathname)` = <environment>,
`extend(AromaChipTypeAnnotationFile(...), c("AffymetrixCdfFile", ` =
<environment>, :
[2010-09-27 06:48:54] Exception: Pathname not found: annotationData/
chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf (none of the parent
directories [annotationData/chipTypes/HuGene-1_0-st-v1/] exist;
current directory is '/Library/Frameworks/R.framework/Versions/2.11/
Resources/library/aroma.affymetrix/annotationData/chipTypes/HuGene-1_0-
st-v1')
at throw(Exception(...))
at throw.default("Pathname not found: ", pathname, reason)
at throw("Pathname not found: ", pathname, reason)
at method(static, ...)
at Arguments$getReadablePathname(filename, path = path, mustExist =
at GenericDataFile(...)
at extend(GenericDataFile(...), "AromaMicroarrayDataFile")
at AromaMicroarrayDataFile(...)
at extend(AromaMicroarrayDataFile(...), c("AffymetrixFile", uses("A
at AffymetrixFile(...)
at extend(AffymetrixFile(...), "AromaChipTypeAnnotationFile")
at AromaChipTypeAnnotationFile(...)
at extend(AromaChipTypeAnnotationFile(...), c("AffymetrixCdfFile",
at Affymetrix
In addition: Warning messages:
1: In is.na(parent) :
is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(parent) :
is.na() applied to non-(list or vector) of type 'NULL'
> pathname <- getPathname(cdf)
> print(pathname)
[1] "annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-
v1,r3.cdf"
> pathname2 <- AffymetrixCdfFile$findByChipType("HuGene-1_0-st-v1", tags="3")
> print(pathname2)
NULL
#######################################
This is my sessionInfo()
R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] oligoClasses_1.10.0 Biobase_2.8.0
[3] aroma.affymetrix_1.7.0 aroma.apd_0.1.7
[5] affxparser_1.20.0 R.huge_0.2.0
[7] aroma.core_1.7.0 aroma.light_1.16.1
[9] matrixStats_0.2.1 R.rsp_0.4.0
[11] R.cache_0.3.0 R.filesets_0.9.0
[13] digest_0.4.2 R.utils_1.5.2
[15] R.oo_1.7.4 oligo_1.12.2
[17] R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] affyio_1.16.0 Biostrings_2.16.5 DBI_0.2-5
[4] IRanges_1.6.6 preprocessCore_1.10.0 splines_2.11.1
[7] tools_2.11.1
####################################
This is my traceback()
6: throw.Exception(Exception(...))
5: throw(Exception(...))
4: throw.default(msg)
3: throw(msg)
2: method(static, ...)
1: AffymetrixCdfFile$fromChipType("HuGene-1_0-st-v1", tags = "r3")
###############################
I would appreciate any help, thanks!!!
Wero.
--
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