I do not know why, but after I converted the custom CDF into binary
CDF and used the binary CDF to do analysis, the analysis went smoothly
without any error message.
Here I still have some questions. First, is there any Vignette/
instruction to illustrate the
further gene expression analysis (high-level analysis?) using the
output of aroma.affymetrix's RMA analysis? Second, what's the usual
gene
expression data analysis work flow (starting with aroma.affymetrix)?
Thanks a lot for the help!
Ying
On Jul 8, 10:33 am, sean nj <njs...@gmail.com> wrote:
> 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
>
>
>
> - Hide quoted text -
>
> - Show quoted text -
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