Hi Minya,
what does sessionInfo() report after library(PSCBS)?
Also, could you please send me (offline; not to the mailinglist) the
following 'MP20120106.Rbin' file:
df - data.frame(chromosome=chromosome, x=x, CT=CT, betaT=betaT,
betaN=betaN);
saveObject(df, MP20120106.Rbin);
/Henrik
On
Hi David,
I've created ACS, UFL and UGP files for the CytoScanHD_Array chip type, but
they are still to be validated. You could start by comparing the content
of yours to mine, which you find at:
http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/incomplete/
/Henrik
Hi David,
it may be that your ACS file (containing probe sequences) is corrupt. What
do you get if you do:
acs - getAromaCellSequenceFile(cdf);
data - getSnpNucleotides(acs, verbose=-50);
The you should see what 'uPos' outputs. It holds the (unique) set of
nucleotide positions identified in
BTW, there is no full CDF for this chiptype; Affymetrix
provides only the CytoScanHD_Array.cdf. The concept of a default and
full CDF was only for GenomeWideSNP_5 and GenomeWideSNP_6, which
basically because after settling on the chip design, Affymetrix discovered
that some probes/SNPs didn't
