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 with SNP6 data.
It seemed that the problem in that case was that the user was not using the
"Full" version of the SNP cdf file. However, I didn't see a "Full" cdf file in
the library files available for CytoscanHD on Affy's website. I'm using
ugp, ufl and acs files that I created myself using NetAffx annotation files
and instructions from the aroma website.
Will I need to edit the CytoscanHD .cdf? What does the uPos variable refer
to?
Cheers,
David
> acc.KR.set <- AllelicCrosstalkCalibration( cs.KR.set, model="CRMAv2")
> csC.KR.set <- process( acc.KR.set, verbose=verbose )
Calibrating data set for allelic cross talk...
Compressing model parameter to a short format...
Compressing model parameter to a short format...done
Calibrating 5 arrays...
Path: probeData/Mandy,KR,set,ACC,ra,-XY/CytoScanHD_Array
Array #1 ('KR 0905 111222_2') of 5...
*Error: length(uPos) > 0 is not TRUE*
Array #1 ('KR 0905 111222_2') of 5...done
Calibrating 5 arrays...done
### Session Info:
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.affymetrix_2.3.0 affxparser_1.24.0 aroma.apd_0.2.0
R.huge_0.3.0 aroma.core_2.3.2
[6] aroma.light_1.22.0 matrixStats_0.4.3 R.rsp_0.7.0
R.cache_0.5.2 R.filesets_1.1.3
[11] digest_0.5.1 R.utils_1.9.7 R.oo_1.8.3
R.methodsS3_1.2.1
### Traceback:
> traceback()
10: stop(paste(ch, " is not ", if (length(r) > 1L) "all ", "TRUE",
sep = ""), call. = FALSE)
9: stopifnot(length(uPos) > 0)
8: getSnpNucleotides.AromaCellSequenceFile(this, cells = cells,
..., verbose = verbose)
7: getSnpNucleotides(this, cells = cells, ..., verbose = verbose)
6: groupBySnpNucleotides.AromaCellSequenceFile(acs, cells = cells,
shifts = shifts, verbose = verbose)
5: groupBySnpNucleotides(acs, cells = cells, shifts = shifts, verbose =
verbose)
4: getSetsOfProbes.AllelicCrosstalkCalibration(this, verbose =
less(verbose,
1))
3: getSetsOfProbes(this, verbose = less(verbose, 1))
2: process.AllelicCrosstalkCalibration(acc.Mandy.KR.set, verbose = verbose)
1: process(acc.Mandy.KR.set, verbose = verbose)
Calibrating data set for allelic cross talk...done
### Data for output of acc:
> print(acc.KR.set)
AllelicCrosstalkCalibration:
Data set: Mandy
Input tags: KR,set
User tags: *
Asterisk ('*') tags: ACC,ra,-XY
Output tags: KR,set,ACC,ra,-XY
Number of files: 5 (328.98MB)
Platform: Affymetrix
Chip type: CytoScanHD_Array
Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200,
subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr
"sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05
0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98)
Output path: probeData/Mandy,KR,set,ACC,ra,-XY/CytoScanHD_Array
Is done: FALSE
RAM: 0.01MB
--
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