Yes,
it should be alright to those annotation data files I've placed on
http://aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/
The attached plot is a proof of concept using an example data set from
Affymetrix.
FYI, *.acs (and *.ugp, and *.ufl) files are binary files, so I do
Sorry Henrik, missed your post from last week. I downloaded your acs file.
It's the same size and the number of rows appear to be the same as the one
I made (as determined by aroma), but there appear to have differences in
file structure:
dgoode$ wc CytoScanHD_Array,HB20111008.acs
11
Ok, so it fails to identify any SNP positions based on your ACS file, cf.
> SNP positions:
> int [1:2410205] NA NA NA NA NA NA NA NA NA NA ...
> Tabulated SNP positions:
> character(0)
> Unique SNP positions:
> integer(0)
My guess is that your ACS file is incorrect (all zeros?). Did you
compare
Thanks, but I'm still having the same problem. Here's what happens:
> acs <- getAromaCellSequenceFile(cdf);
> cells <- getAlleleCellPairs(cdf, verbose=verbose);
Identifying the probe pairs...
Units:
NULL
Checking for cached results...
Found cached results
Checking for cached results...done
Sorry,
that should have been:
acs <- getAromaCellSequenceFile(cdf);
cells <- getAlleleCellPairs(cdf, verbose=verbose);
data <- getSnpNucleotides(acs, cells=cells, verbose=-50);
Look for the "Unique SNP positions:" output.
/Henrik
On Sun, Jan 8, 2012 at 3:23 PM, D Goode wrote:
> Hi Henrik,
>
>
Hi Henrik,
Thanks for getting back to me.
I get another error message when I run the commands you suggested:
> acs <- getAromaCellSequenceFile(cdf);
> data <- getSnpNucleotides(acs, verbose=-50);
Error in is.matrix(cells) : 'cells' is missing
David
--
When reporting problems on aroma.affy
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 di
I'm trying to process some data from CytoscanHD arrays but run into an
error ("Error: length(uPos) > 0 is not TRUE") when trying to process the
output from AllelicCrosstalkCalibration. Details, including traceback &
sessionInfo below.
I saw a post from another user who received a similar error
