Dear list,
I am using aroma.affymetrix to normalize GenomeWideSNP_6 data.
I have setup the library and CEL files as described on the website.
When I am trying to execute the following block...
acc <- AllelicCrosstalkCalibration(cs, model="CRMAv2");
print(acc);
cs.C <- process(acc, verbose=log);
print(cs.C);
I get the following error while processing the first sample:
20110607 19:01:08| Fitting...done
20110607 19:01:08| Allele probe-pair group #7 ('missing') of
7...done
20110607 19:01:08| Fitting calibration model...done
20110607 19:01:08| Estimated origins:
A/C A/G A/T C/G C/T G/T missing
A 129.1 153.8 132.8 165.0 213.2 136.1 141
B 139.9 113.2 107.6 117.5 160.6 149.1 137
20110607 19:01:08| Weighted average offset: 153.30
20110607 19:01:08| Backtransforming (calibrating) data...
20110607 19:01:08| Allele basepair #1 ('A/C') of 7...
20110607 19:01:08| Allele basepair #1 ('A/C') of 7...done
20110607 19:01:08| Allele basepair #2 ('A/G') of 7...
20110607 19:01:08| Allele basepair #2 ('A/G') of 7...done
20110607 19:01:08| Allele basepair #3 ('A/T') of 7...
20110607 19:01:09| Allele basepair #3 ('A/T') of 7...done
20110607 19:01:09| Allele basepair #4 ('C/G') of 7...
20110607 19:01:09| Allele basepair #4 ('C/G') of 7...done
20110607 19:01:09| Allele basepair #5 ('C/T') of 7...
20110607 19:01:09| Allele basepair #5 ('C/T') of 7...done
20110607 19:01:09| Allele basepair #6 ('G/T') of 7...
20110607 19:01:10| Allele basepair #6 ('G/T') of 7...done
20110607 19:01:10| Allele basepair #7 ('missing') of 7...
20110607 19:01:10| Allele basepair #7 ('missing') of 7...done
20110607 19:01:10| Backtransforming (calibrating) data...done
20110607 19:01:10| Correcting offset for all non-SNP cells...
20110607 19:01:10| Cells:
int [1:964281] 3466656 3466655 3463975 3463976 3461296 3461295
3458616 3458615 3455936 3455935 ...
20110607 19:01:10| Offset: 153.301161350039
20110607 19:01:10| Correcting offset for all non-SNP cells...done
Error in rescale(this, yAll = yAll, params = params, setsOfProbes =
setsOfProbes, :
unused argument(s) (yAll = yAll, params = params, setsOfProbes =
setsOfProbes, verbose = less(verbose))
20110607 19:01:10| Array #1 ('37A55') of 46...done
20110607 19:01:10| Calibrating 46 arrays...done
20110607 19:01:10|Calibrating data set for allelic cross talk...done
Then the script halts.
I tried using the doCRMAv2 wrapper, with the same result.
I tried using another dataset, and got the same error.
I also tried re-installing aroma.affymetrix and aroma.cn.
> hbInstall("aroma.affymetrix")
> hbInstall("aroma.cn")
(I do not get this error while analyzing Mapping250K_{Nsp,Sty} data
with a similar script.)
> aroma.affymetrix
[1] "AromaAffymetrix: aroma.affymetrix v2.1.0 (2011-04-08) is loaded
(pos=9).
> aroma.cn
[1] "Package: aroma.cn v0.5.2 (2010-08-04) is loaded (pos=2).
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] aroma.cn_0.5.2 sfit_0.2.0
bioinf_1.0
[4] ggplot2_0.8.9 proto_0.3-8
reshape_0.8.4
[7] plyr_1.4 aroma.affymetrix_2.1.0
aroma.apd_0.1.8
[10] affxparser_1.22.1 R.huge_0.2.2
aroma.core_2.1.0
[13] aroma.light_1.20.0 matrixStats_0.2.2
R.rsp_0.5.3
[16] R.cache_0.4.2 R.filesets_1.0.1
digest_0.5.0
[19] R.utils_1.7.5 R.oo_1.8.0
R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.13.0
--
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