[BioC] crlmm : copy number and genotyping of Illumina data

[Matt Ritchie]

Dear Abhi,

You're using the appropriate function.  Judging by the warning message, it looks like one of your samples is not like the others (i.e. sample 6431_8116121004 is not Omni5 version 1b).

Maybe try leaving that one out and re-running?  If that doesn't help, perhaps you could put the idat files for this test set of 5 arrays online so that I can take a closer look.

Best wishes,

Matt

----- Original Message -----
From: "Abhishek Pratap" <apratap at sagebase.org>
To: bioconductor at r-project.org
Sent: Tuesday, 18 February, 2014 11:01:38 AM
Subject: [BioC] crlmm : copy number and genotyping of Illumina data

Hi All

I am trying to use crlmm package for doing the genotyping and CNV
analysis on a set ~200 samples genotyped on Illumina Omni5 array.


I tried following the vignette (seems a  bit dated) and got some
errors(see below)
http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/inst/doc/IlluminaPreprocessCN.pdf

Also searching a bit more I found multiple functions in the code of
crlmm like (genotype.Illumina, crlmmIlluminav2 etc) which seem to be
doing similar stuff.

Just wondering if someone can point me to the latest recipe(if any) of
reading in the idat files (dual channel) and do the basic genotyping
calling + copy number analysis.


here is what I have done for a test case (5 arrays)


> cnSet <- genotype.Illumina(sampleSheet = samplesheet[1:5,],
+                            arrayNames = arrayNames[1:5],
+                            arrayInfoColNames =
list(barcode="SentrixBarcode_A", position="SentrixPosition_A"),
+                            path = datadir,
+                            copynumber = T,
+                            batch = samplesheet$Sample_Group[1:5],
+                            cdfName = "humanomni5quadv1b",
+                            call.method = "krlmm",
+                            verbose=T
+                           )
Instantiate CNSet container.
Initializing container for genotyping and copy number estimation
reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5396_6298080101_R02C01_Grn.idat
reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5405_6298080103_R03C01_Grn.idat
reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5414_6298098003_R04C01_Grn.idat
reading /work/DAT_118__AML/Analysis/dset1/CNV/data/6431_8116121004_R03C01_Grn.idat
reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5423_6762372017_R01C01_Grn.idat
Processing sample stratum 1 of 1

Loading chip annotation information.
Loading reference normalization information.
Quantile normalizing 5 arrays, one at a time.
  |===============================================================================================|
100%
Loading snp annotation and mixture model parameters.
Calibrating 5 arrays.
  |=========================================================
                           |  60%
Error in quantile.default(M, c(1, 5)/6, names = FALSE) :
  missing values and NaN's not allowed if 'na.rm' is FALSE

In addition: Warning messages:
1: In getProtocolData.Illumina(grnidats, sep = sep, fileExt = fileExt$green,  :
  Chips are not of the same type.  Skipping 6431_8116121004_R03C01_Grn.idat
2: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames =
arrayNames[sel],  :
  Chips are not of the same type.  Skipping
6431_8116121004_R03C01_Grn.idat and 6431_8116121004_R03C01_Red.idat




Thanks!
-Abhi

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