Hi all, 

 

Please bear with me as I am still new to beadarraySNP. I have a rather
large SNP dataset (normal/tumor pairs) from iLLUMINA Human610-Quad
beadchips. For the moment I am interested in doing simple copynumber/LOH
analysis on the data set however I seem to get into trouble when
plotting these, most likely as a result of "NA's" being introduced into
the data set. 

 

I use BeadStudio to create a FinalReport with the following fields:

'SNP Name', 'Sample ID', 'GC Score', 'Allele1 - AB', 'Allele2 - AB', 'GT
Score', 'X Raw',  'Y Raw', 'Chr' and 'Position'

 

I also use it to create the sample_map file and manually add a "NorTum"
column to it (this fixed some previous errors I was getting).

 

The data reads in without errors using:
read.SnpSetIllumina(Sample_Map2Samplesheet("Sample_Map.txt"),
reportfile="FinalReport.txt")

 

The normalization process runs with warnings.

 

>SNPnrm <- normalizeBetweenAlleles.SNP(mydata4)

Loading required package: limma

> SNPnrm <- normalizeWithinArrays.SNP(SNPnrm, callscore = 0.8, relative
= TRUE, fixed = FALSE, quantilepersample = TRUE)

Warning message:

In numericCHR(pData(featureData(object))[, "CHR"]) :

  NAs introduced by coercion

> SNPnrm <- normalizeLoci.SNP(SNPnrm, normalizeTo = 2)

Warning message:

In atan2(y, x) : NaNs produced

 

Finally when I try to plot the copyNumber things start going wrong.
While the first sample seems to plot without any trouble the subsequent
plots fail.

 

>reportSamplesSmoothCopyNumber(SNPnrm, normalizedTo = 2, smooth.lambda =
4)

Error in tmp.resp[1:ol] * portion : 

  non-numeric argument to binary operator

 

as well as 20 error messages stating:

In .quantsmooth(intensities[i.s:i.e], smooth.lambda, tau,  ... :

  data is all NA, result is NA

 

I also can't run the copynumberConversion tool, with errors as follows:

 

Error in `[.data.frame`(fData(object), , c("snpid", "IllCode", "CHR",  :


  undefined columns selected

 

Is there anything specific that I should check for or anything that I am
doing in the wrong order. Any advice is more than welcome.

 

Thank you in advace.

 

 

Dmitri Mouradov

 

Bioinformatician 

Ludwig Colon Cancer Initiative Laboratory

PO Box 2008

Royal Melbourne Hospital

VIC 3050, Australia

 

Ph.: +61 (0) 3 93413155
Fax: +61 (0) 3 93413104

 



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