Hi,
I hope I am not asking a too simple question but I am trying to load
affy HuGene-1_1-st-v1 chips on aroma.affymetrix. I have been away from
affy analysis for a while so maybe this is a known thing. I cannot
find the corresponding cdf file (in affymetrix webpage they seem to
have modified the files). I tried with the HuGene-1_0-st-v1 cdf file
(which seems to work for dChip analysis) renaming it but gave me an
error:
> cdf <- AffymetrixCdfFile$byChipType("HuGene-1_1-st-v1")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuGene-1_1-st-v1
Filename: HuGene-1_1-st-v1.cdf
Filesize: 16.67MB
Chip type: HuGene-1_1-st-v1
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1050x1050
Number of cells: 1102500
Number of units: 33252
Cells per unit: 33.16
Number of QC units: 0
> chipType <- "HuGene-1_1-st-v1"
> cs <- AffymetrixCelSet$byName("Samples", cdf=cdf)
Error en method(static, ...) :
[2012-06-11 17:15:28] Exception: Failed to setup a data set for any of
1 data directories located. The following reasons were reported: (1)
Cannot set CDF. The specified CDF structure ('HuGene-1_1-st-v1') is
not compatible with the chip type ('HuGene-1_1-st-v1') of the CEL
file. The number of cells do not match: 1102500 != 1178100 (while
trying 'rawData/Samples/HuGene-1_1-st-v1').
Can anyone help me?
Thanks
Dave
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] hugene11stv1hsentrezgcdf_15.1.0 AnnotationDbi_1.16.19
Biobase_2.14.0
[4] aroma.affymetrix_2.5.0 affxparser_1.26.4
aroma.apd_0.2.2
[7] R.huge_0.3.0 aroma.core_2.5.0
aroma.light_1.22.0
[10] BiocInstaller_1.2.1 matrixStats_0.5.0
R.rsp_0.7.5
[13] R.cache_0.6.2 R.filesets_1.1.5
digest_0.5.2
[16] R.utils_1.12.1 R.oo_1.9.3
affy_1.32.1
[19] R.methodsS3_1.2.2
loaded via a namespace (and not attached):
[1] affyio_1.22.0 DBI_0.2-5 IRanges_1.12.6
preprocessCore_1.16.0 RSQLite_0.11.1
[6] tools_2.14.1 zlibbioc_1.0.1
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