Hi,
I can reproduce this. It is because of a name clash between ggplot2
and aroma.affymetrix; both defines a rescale() method. Try to avoid
loading ggplot2 and it should work. (Alternatively, make sure to load
ggplot2 *before* aroma.affymetrix and add rescale.numeric <-
ggplot2::rescale). I'll see if I can add an automatic workaround for
this in the next release.
The reason why it works with Mapping250K_{Nsp,Sty} data is that the
defaults for the crosstalk correction methods are slightly different
for those chip types and therefor no "rescaling" is done.
/Henrik
On Tue, Jun 7, 2011 at 4:10 PM, David JH Shih <david.s...@utoronto.ca> wrote:
> 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
>
>
>
>
>
> --
> 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.
You received this message because you are subscribed to the Google Groups
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