Hi;

When one uses readCelUnits() to read SNP chip cel files, how one can  
tell which values are for forward strand or for backward strand and  
which values are from the non-shifted probes or from the shifted  
probes? For instance, in the following code chunk, which values are  
from forward/backward strand and from central/shifted probes?

library("hapmap100kxba", lib="~/Library/R64")
library(affxparser, lib="~/Library/R64")

pth <- system.file('celFiles', package='hapmap100kxba')
files <- list.files(path=pth, full.names=T)

chip.type <- readCelHeader(files[1])$chiptype  ## Mapping50K_Xba240
cels <- readCelUnits(files[1], cdf='~/Project/ProbeAnnot/ 
Mapping50K_Xba240.cdf', stratifyBy='pm', addDimnames=T)
length(cels)  ## 59015
labs.test <- names(cels)[100:120]
cels[[labs.test[1]]]
## $A
## $A$intensities
## [1]  7563  8050  9531  9292 11261
##
## $G
## $G$intensities
## [1]  6540  7639  9027 10512 11381
##
## $A
## $A$intensities
## [1] 4036 4144 3858 5170 3975
##
## $G
## $G$intensities
## [1] 4425 4291 3682 5912 5208


Tae-Hoon Chung

Post-Doctoral Researcher
Computational Biology Division, TGEN
445 N 5th St. Phoenix, AZ 85004 USA
O: 1-602-343-8724
F: 1-602-343-8840



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