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
Identifying the probe pairs...done
> data <- getSnpNucleotides(acs, cells=cells, verbose=-50);
Retrieving SNP nucleotides...
Probe shifts:
int 0
Argument 'cells':
int [1:2, 1:2410205] 702209 3820208 6174755 2915229 1437029 2981430
4652935 141307 3892235 1614497 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:2] "A" "B"
..$ : NULL
Number of pairs: 2410205
Identifying SNP positions of cell allele pairs...
Checking for cached results...
Found cached results
Checking for cached results...done
Identifying SNP positions of cell allele pairs...done
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)
Error: length(uPos) > 0 is not TRUE
Retrieving SNP nucleotides...done
### Details of the acs
> acs
AromaCellSequenceFile:
Name: CytoScanHD_Array
Tags: 20120104
Full name: CytoScanHD_Array,20120104
Pathname:
annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,20120104.acs
File size: 170.91 MB (179217220 bytes)
RAM: 0.00 MB
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20120106 12:16:17
EST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType>
Chip type: CytoScanHD_Array
Platform: Affymetrix
### Session info & traceback
> 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()
4: stop(paste(ch, " is not ", if (length(r) > 1L) "all ", "TRUE",
sep = ""), call. = FALSE)
3: stopifnot(length(uPos) > 0)
2: getSnpNucleotides.AromaCellSequenceFile(acs, cells = cells, verbose =
-50)
1: getSnpNucleotides(acs, cells = cells, verbose = -50)
--
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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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