On Thu, Sep 3, 2009 at 1:28 AM, JeromeW<[email protected]> wrote:
>
>
>
>> > library("aroma.affymetrix");
>> > pathname <-
>> > "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";
>> > cdf <- AffymetrixCdfFile(pathname);
>
> This works!
> Thank you Henrik.
No, no, that is supposed to be a a workaround - it is only for
troubleshooting! You should never ever have to specify paths in your
scripts, so don't consider the above as an option.
So, the CDF is located in the correct place. Continuing:
pathname <- "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";
cdf <- AffymetrixCdfFile(pathname);
pathname <- getPathname(cdf);
print(pathname);
pathname2 <- AffymetrixCdfFile$findByChipType("GenomeWideSNP_6", tags="Full");
print(pathname2);
# The two pathnames should be the same
stopifnot(identical(pathname2, pathname));
If they are, then this *should* work:
cdf2 <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
print(cdf2);
Does it? If not, what does this give:
path <- getPath(cdf);
cat(list.files(path=path), sep="\n");
/Henrik
> >
>
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