Thank you Henrik and Pierre. I am able to run it successfully now.
It gives me a few warnings at the end.
> warnings()
Warning messages:
1: In log2(y) : NaNs produced
2: In log2(y) : NaNs produced
3: In log2(y) : NaNs produced
4: In log2(y) : NaNs produced
5: In log2(y) : NaNs produced
6: In log2(y) : NaNs produced
7: In log2(y) : NaNs produced
8: In log2(y) : NaNs produced
9: In log2(y) : NaNs produced
10: In log2(y) : NaNs produced
11: In log2(y) : NaNs produced
12: In log2(y) : NaNs produced
13: In log2(y) : NaNs produced
14: In log2(y) : NaNs produced
15: In log2(y) : NaNs produced
16: In log2(y) : NaNs produced
17: In log2(y) : NaNs produced
18: In log2(y) : NaNs produced
19: In log2(y) : NaNs produced
20: In log2(y) : NaNs produced
21: In log2(y) : NaNs produced
22: In log2(y) : NaNs produced
23: In log2(y) : NaNs produced
24: In log2(y) : NaNs produced
Any suggestions as to how to avoid them and what they mean with respect to
doCRMAv2 ?
Thanks
Nitesh
On Monday, 18 June 2012 16:58:19 UTC-4, NT_CMU wrote:
>
> Hi
>
> I'm trying to run the command "doCRMAv2", and i get these errors. Let me
> know what the problem is, if any of you have encountered this before. I
> thought i did not have some library installed but, i have both ACNE and
> aroma.affymetrix working properly.
>
> > ds <- doCRMAv2("LeeAV_2012",chipType="GenomeWideSNP_6,Full")
> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
> [2012-06-18 16:55:10] Exception: Failed to retrieve genome information for
> this chip type: GenomeWideSNP_6
>
> at #12. getGenomeInformation.AffymetrixCdfFile(cdf)
> - getGenomeInformation.AffymetrixCdfFile() is in environment
> 'aroma.affymetrix'
>
> at #11. getGenomeInformation(cdf)
> - getGenomeInformation() is in environment 'aroma.affymetrix'
>
> at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this)
> - getSubsetToAvg.AllelicCrosstalkCalibration() is in environment
> 'aroma.affymetrix'
>
> at #09. getSubsetToAvg(this)
> - getSubsetToAvg() is in environment 'aroma.affymetrix'
>
> at #08. getParameters.AllelicCrosstalkCalibration(this)
> - getParameters.AllelicCrosstalkCalibration() is in environment
> 'aroma.affymetrix'
>
> at #07. getParameters(this)
> - getParameters() is in environment 'R.rsp'
>
> at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose)
> - process.AllelicCrosstalkCalibration() is in environment
>
>
> Thanks
>
> Nitesh
>
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