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
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
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
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
OK, I think I worked it out. I've created UFL & UPG files for the CytoScan
HD and am working on building an ACS file.
Can anyone recommend some sanity checks I could carry out to make sure I
did this properly? Everything seems fine when I double-check the data for a
few randomly selected probe
Has anyone successfully used aroma.affymetrix with Cytoscan HD array data?
I downloaded the .cdf for the Cytoscan arrays from Affy and managed to read
it in, but failed at the getGenomeInformation() step. The error was "Failed
to retrieve genome information for this chip type". R output is below
