[BioC] affyxparser package question

[Benilton Carvalho]

any specific reason to not use

library(oligo)
x = read.celfiles(list.celfiles())

and check the annotation packages?

b

On Aug 8, 2007, at 6:02 PM, Tae-Hoon Chung wrote:

> 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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