Hi all
I reply in this thread because I also have the could not locate a
file problem which I cannot solve.
My code:
setwd(/x05/people/m140932/eclipse/workspace/CNV); # here I set the
working directory
library(aroma.affymetrix);
log - verbose - Arguments$getVerbose(-8, timestamp=TRUE);
(sorry for quoting myself)
I am more and more puzzled... The findByChipType method seems to
correctly detect the cdf file:
AffymetrixCdfFile$findByChipType(GenomeWideSNP_6, tags=Full)
[1] annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full.cdf
No worries at all - I just want you and everyone else to know how to
make this forum more effective, which is somewhat explained in that
FAQ. 2008-03-26:
http://groups.google.com/group/aroma-affymetrix/web/frequently-asked-questions
Cheers,
Henrik
On Tue, Sep 1, 2009 at 11:58 AM,
So, if none of the stopifnot() tests complaints, then it might be that
the CDF file might be corrupt or incomplete. Compare with the file
size and checksum that I get:
library(aroma.affymetrix);
pathname -
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf;
df -
Hi.
On Tue, Sep 1, 2009 at 10:04 PM, Max Moldovanmax.moldo...@gmail.com wrote:
Hi People,
I have the following sequence of commands:
chipType - GenomeWideSNP_5;
cdfTags - Full,r2;
cdf - AffymetrixCdfFile$byChipType(chipType, tags=cdfTags)
print(cdf)
gi - getGenomeInformation(cdf)
Hi.
On Wed, Sep 2, 2009 at 8:56 PM, Max Moldovanmax.moldo...@gmail.com wrote:
Thanks for your information Henrik.
1. I can extract sigma estimates using you first suggestion:
rawCNs - extractRawCopyNumbers(cbs, array=3, chromosome=9);
sigma - estimateStandardDeviation(rawCNs);
A
