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 all probes. Typically it is position 13
in the 25mers, but for some chip types it is off a few bases for some
probes. However, they should at least have some positions, which is what
this internal sanity check is asserting.
/Henrik
On Friday, January 6, 2012, D Goode wrote:
>
> 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
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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