Hi guys,
I have a weird situation that I need to retrieve probe level intensity (not
the probeset/gene level) from U133Plus2 expression array data. I did RBC
and qn first.
> library(aroma.affymetrix)
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> chipType <- "HG-U133_Plus_2,Binary,Hs_ENTREZG"
> cdf <- AffymetrixCdfFile$byChipType(chipType)
> cs <- AffymetrixCelSet$byName("Genesis_Lung", cdf=cdf)
> bc <- RmaBackgroundCorrection(cs)
> csBC <- process(bc,verbose=verbose)
> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> csN <- process(qn, verbose=verbose)
> print(csN)
.....
At first, I tried to save the data into a table, but had no success.
> data <- readUnits(csN)
> write.table(data,"myfile.txt",sep="\t")
Error in data.frame(`AFFX-BioB-5_at` = list(`AFFX-BioB-5_at` =
list(intensities = c(6.21948575973511, :
arguments imply differing number of rows: 40, 22, 138, 16, 38, 108, 28,
42, 36, 44, 18, 64, 20, 60, 14, 32, 34, 24, 10, 8, 12, 48, 6, 46, 128, 106,
54, 26, 52, 88, 56, 62, 82, 66, 70, 74, 76, 58, 86, 30, 78, 80, 96, 102,
84, 142, 50, 100, 116, 110, 68, 146, 120, 90, 98, 92, 148, 134, 122, 118,
72, 144, 126, 104, 150, 124, 162, 136, 130, 114, 94, 112, 132, 216, 154,
140, 168, 172, 152, 160, 170, 182, 178, 166, 180, 198
>
Then, I tried some method metioned in thread regarding exon array (
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/40e3950e52d73c1f
)
> cell <- 9049 # 9049 is the unit number corresponding to the probeset
3799_at in custom CDF
> Y <- extractMatrix(csN, cells=cells, field=c("intensities", "stdvs",
"pixels"), drop=FALSE, verbose=verbose)
Error in extractMatrix.AffymetrixCelSet(csN, cells = cells, field =
c("intensities", :
object 'cells' not found
At last, I repeated the above without "cells=cells" and it seemed working
with no error message. But I am not sure if this is the right result or not.
> Y <- extractMatrix(csN, field=c("intensities", "stdvs", "pixels"),
drop=FALSE, verbose=verbose)
Any suggestion?
Thanks a lot for the help!
Sean
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