Hi guys,
I am new to the aroma.affymetrix package. Here I try to do RMA on
affy HG-U133_Plus_2 chip CEL files. I can proceed without problem by
using Henrik's HG-U133_Plus_2,Binary,HB.cdf. But when I tried to use
BrainArray's custom CDF(Hs133P_Hs_REFSEQ.CDF from the aroma-
project.org website) as the CDF for my analysis, I got the error
message. So I
downloaded the newest version HG-U133_Plus_2,Hs_ENTREZG.cdf from
BrainArray website and aroma.affymetrix took it as a CDF correctly.
But when I tried to do
> cs <- AffymetrixCelSet$byName("My_Met_Melanoma", cdf=cdf)
I got the error message again:
Error in list(`AffymetrixCelSet$byName("My_Met_Melanoma", cdf =
cdf)` = <environment>, :
Exception: Failed to setup a data set for any of 1 data
directories located......
I tried doRMA() and got the same error.
What did I do wrong? Any suggestion?
One more question, is there a Vignette/instruction to illustrate the
further gene expression analysis (high-level analysis?) using the
output of aroma.affymetrix's RMA analysis? Or what's the usual gene
expression data analysis work flow (starting with aroma.affymetrix)?
Thanks a lot for the help!
Ying
> chipType <- "HG-U133_Plus_2"
> cdf <- AffymetrixCdfFile$byChipType("Hs133P_Hs_REFSEQ")
Error in list(`AffymetrixCdfFile$byChipType("Hs133P_Hs_REFSEQ")` =
<environment>, :
[2011-07-08 09:45:36] Exception: Could not locate a file for this chip
type: Hs133P_Hs_REFSEQ
at throw(Exception(...))
at throw.default("Could not locate a file for this chip type: ",
paste(c(chipTyp
at throw("Could not locate a file for this chip type: ",
paste(c(chipType, tags)
at method(static, ...)
at AffymetrixCdfFile$byChipType("Hs133P_Hs_REFSEQ")
> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2,Hs_ENTREZG")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HG-U133_Plus_2
Filename: HG-U133_Plus_2,Hs_ENTREZG.cdf
Filesize: 45.03MB
Chip type: HG-U133_Plus_2,Hs_ENTREZG
RAM: 0.00MB
File format: v3 (text; ASCII)
Dimension: 1164x1164
Number of cells: 1354896
Number of units: 19070
Cells per unit: 71.05
Number of QC units: 9
> cs <- AffymetrixCelSet$byName("My_Met_Melanoma", cdf=cdf)
Error in list(`AffymetrixCelSet$byName("My_Met_Melanoma", cdf = cdf)`
= <environment>, :
[2011-07-08 09:49:19] Exception: Failed to setup a data set for any of
1 data directories located.
at throw(Exception(...))
at throw.default(sprintf("Failed to setup a data set for any of %d
data director
at throw(sprintf("Failed to setup a data set for any of %d data
directories loca
at method(static, ...)
at AffymetrixCelSet$byName("My_Met_Melanoma", cdf = cdf)
> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2",tags="Binary,HB")
> cs <- AffymetrixCelSet$byName("My_Met_Melanoma", cdf=cdf)
> ds <- doRMA("My_Met_Melanoma", chipType="HG-U133_Plus_2,Hs_ENTREZG")
Error in list(`doRMA("My_Met_Melanoma", chipType = "HG-
U133_Plus_2,Hs_ENTREZG")` = <environment>, :
[2011-07-08 10:05:57] Exception: Failed to setup a data set for any of
1 data directories located.
at throw(Exception(...))
at throw.default(sprintf("Failed to setup a data set for any of %d
data directories located.", lengt
at throw(sprintf("Failed to setup a data set for any of %d data
directories located.", length(paths)
at method(static, ...)
at AffymetrixCelSet$byName(dataSet, ..., verbose = less(verbose,
50), .onUnknownArgs = "ignore")
at doRMA.character("My_Met_Melanoma", chipType = "HG-
U133_Plus_2,Hs_ENTREZG")
at doRMA("My_Met_Melanoma", chipType = "HG-U133_Plus_2,Hs_ENTREZG")
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252
LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] aroma.affymetrix_2.1.0 aroma.apd_0.1.8
affxparser_1.24.0 R.huge_0.2.2
[5] aroma.core_2.1.0 aroma.light_1.20.0
matrixStats_0.2.2 R.rsp_0.5.4
[9] R.cache_0.4.2 R.filesets_1.0.2
digest_0.5.0 R.utils_1.7.5
[13] R.oo_1.8.0 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.13.0
>
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