The information the cdf file is giving me seems misleading:
nbrOfCells(cdf)
# 4,691,556
cellIndices <- getCellIndices(cdf)
#length(unlist(cellIndices))
# 4,358,832
The number of cells does not match the cell indices. ??
On May 18, 7:41 pm, Irene Pylypenko <ipylype...@gmail.com> wrote:
> chipType <- "Hs_PromPR_v02"
> cdf <- AffymetrixCdfFile$byChipType(chipType, verbose=verbose)
> cs <- AffymetrixCelSet$byName("GSE17125", cdf=cdf, verbose=verbose)
> acp <- AromaCellPositionFile$byChipType(chipType)
> #dim 4359744 2
> data <- extractMatrix(cs)
> #dim: 4691556 66
>
> On May 17, 5:29 pm, Henrik Bengtsson <henrik.bengts...@aroma-
>
> project.org> wrote:
> > Hi,
>
> > which chip type and CDF are you thinking of? Even better, please show
> > the code how you got those numbers and we take it from there.
>
> > /Henrik
>
> > On Tue, May 17, 2011 at 1:53 PM, Irene Pylypenko <ipylype...@gmail.com>
> > wrote:
> > > Hello,
> > > How do I find the genomic location of each probe (cell)? Specifically,
> > > a chromosome # and start site. Is this information stored in a
> > > AffymetrixCelSet object?
> > > I know the cdf object contains this information, via the
> > > AromaCellPositionFile file, but this gives me 4,359,744 probes, where
> > > as AffymetrixCelSet gives me 4,691,556. So I was wondering how I could
> > > map these two files.
> > > I know about the UGP files, but I believe it gives the unit locations,
> > > whereas I'm interested in probe location.
> > > Thanks,
> > > Irene
>
> > > --
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> > > and traceback(), and 3) to post a complete code example.
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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