Hi Matt

As it happens this got on the back burner earlier and I am getting back to
it now. I am getting similar errors trying to do the CNV analysis on
Illumina Omni5 idat files.  I would be more than happy to share subset of
data with you. Just wondering if you would have time now to help with this.


Depending on the subset of idat files I choose I am getting different
errors.

Example:

#1

leaving out novariant SNPsStart calculating Prior MeansError in
calculatePriorValues(M, numSNP, verbose) :
  could not find function "makeCluster"


#2

Instantiate CNSet container.Initializing container for genotyping and
copy number estimationProcessing sample stratum 1 of 1Quantile
normalizing 12 arrays, one at a time.
|==========================================================================|
100%Calibrating 12 arrays.  |==================
                                |  25%Error in
chol.default(crossprod(sweep(matS, 1, z[, 1], FUN = "*"), matS)) :
  the leading minor of order 1 is not positive definiteIn addition:
Warning messages:1: 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.idat2:
In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames =
arrayNames[sel],  :
  Chips are not of the same type.  Skipping
6440_8116121004_R04C01_Grn.idat and 6440_8116121004_R04C01_Red.idat3:
In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames =
arrayNames[sel],  :
  Chips are not of the same type.  Skipping
6449_8116121005_R01C01_Grn.idat and 6449_8116121005_R01C01_Red.idat


Thanks!
-Abhi


On Tue, Feb 18, 2014 at 8:28 PM, Matt Ritchie <mritchie@wehi.edu.au> wrote:

> 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@sagebase.org>
> To: bioconductor@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
>
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:10}}

