aah I seee. let me do that and get back to you guys. Cheers! -Abhi On Thu, Jun 5, 2014 at 10:59 PM, Matt Ritchie wrote: > Hi Abhi, > > The issue is likely to do with your small (n=3) samples size (less than 8 > and our new method, which uses k-means - > http://www.biomedcentral.com/1471-2105/15/158/abstract will not be > happy). We'll add an error message explaining this to the code. > > If adding a few mores samples doesn't help, perhaps you can provide us > with a subset of your idat files (offline) so that we can have a go at > reproducing this error. > > Cheers, > > Matt > ------------------------------ > *From: *"Abhishek Pratap" > *To: *"Matt Ritchie" > *Cc: *bioconductor@r-project.org > *Sent: *Friday, 6 June, 2014 6:19:51 AM > > *Subject: *Re: [BioC] crlmm : copy number and genotyping of Illumina data > > Hey Matt > > > Here is the most recent error I got > > Instantiate CNSet container.Initializing container for genotyping and copy number estimationProcessing sample stratum 1 of 1Quantile normalizing 3 arrays, one at a time. |===============================================================================================| 100%Calibrating 3 arrays. |===============================================================================================| 100%Finished preprocessing.Preprocessing complete. Begin genotyping...Start computing log ratio -- Processing segment 1 out of 9 -- Processing segment 2 out of 9 -- Processing segment 3 out of 9 -- Processing segment 4 out of 9 -- Processing segment 5 out of 9 -- Processing segment 6 out of 9 -- Processing segment 7 out of 9 -- Processing segment 8 out of 9 -- Processing segment 9 out of 9Done computing log ratioleaving out novariant SNPsStart calculating Prior MeansError in checkForRemoteErrors(val) : > 8 nodes produced errors; first error: number of cluster centres must lie between 1 and nrow(x) > > > > On Thu, Jun 5, 2014 at 12:36 PM, Abhishek Pratap > wrote: > >> Here it is. hopefully the formatting is not that bad >> >> -A >> >> >> > sessionInfo()R version 3.1.0 (2014-04-10) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C >> [5] LC_MONETARY=C LC_MESSAGES=C LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C >> >> attached base packages: >> [1] tools grid parallel stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] synapseClient_1.2-1 affy_1.42.2 frma_1.16.0 >> [4] GEOquery_2.30.0 Biobase_2.24.0 RColorBrewer_1.0-5 >> [7] gplots_2.13.0 samr_2.0 matrixStats_0.8.14 >> [10] impute_1.38.1 ggplot2_1.0.0 VennDiagram_1.6.5 >> [13] DESeq2_1.4.5 RcppArmadillo_0.4.300.0 Rcpp_0.11.1 >> [16] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 IRanges_1.22.7 >> [19] BiocGenerics_0.10.0 illuminaio_0.6.0 gdata_2.13.3 >> [22] ff_2.2-13 bit_1.1-12 humanomni5quadv1bCrlmm_1.0.0 >> [25] crlmm_1.22.0 preprocessCore_1.26.1 oligoClasses_1.26.0 >> [28] BiocInstaller_1.14.2 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.26.0 Biostrings_2.32.0 DBI_0.2-7 KernSmooth_2.23-12 >> [5] MASS_7.3-33 Matrix_1.1-3 R.methodsS3_1.6.1 RCurl_1.95-4.1 >> [9] RJSONIO_1.2-0.2 RSQLite_0.11.4 RcppEigen_0.3.2.1.2 VGAM_0.9-4 >> [13] XML_3.98-1.1 XVector_0.4.0 affxparser_1.36.0 affyio_1.32.0 >> [17] annotate_1.42.0 base64_1.1 bitops_1.0-6 caTools_1.17 >> [21] codetools_0.2-8 colorspace_1.2-4 digest_0.6.4 ellipse_0.3-8 >> [25] foreach_1.4.2 genefilter_1.46.1 geneplotter_1.42.0 gtable_0.1.2 >> [29] gtools_3.4.1 iterators_1.0.7 lattice_0.20-29 locfit_1.5-9.1 >> [33] munsell_0.4.2 mvtnorm_0.9-99992 oligo_1.28.2 plyr_1.8.1 >> [37] proto_0.3-10 reshape2_1.4 scales_0.2.4 splines_3.1.0 >> [41] stats4_3.1.0 stringr_0.6.2 survival_2.37-7 xtable_1.7-3 >> [45] zlibbioc_1.10.0 >> >> >> >> On Tue, Jun 3, 2014 at 4:59 PM, Matt Ritchie >> wrote: >> >>> Dear Abhi, >>> >>> Can you provide your sessionInfo()? >>> >>> Thanks, >>> >>> Matt >>> ------------------------------ >>> *From: *"Abhishek Pratap" >>> *To: *"Matt Ritchie" >>> *Cc: *bioconductor@r-project.org >>> *Sent: *Tuesday, 3 June, 2014 1:36:20 PM >>> *Subject: *Re: [BioC] crlmm : copy number and genotyping of Illumina >>> data >>> >>> >>> 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 >>> 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" >>>> 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 intended solely for >>>> the addressee. >>>> You must not disclose, forward, print or use it without the permission >>>> of the sender. >>>> ______________________________________________________________________ >>>> >>> >>> >>> >>> ______________________________________________________________________ >>> The information in this email is confidential and intended solely for >>> the addressee. >>> You must not disclose, forward, print or use it without the permission >>> of the sender. >>> ______________________________________________________________________ >>> >> >> > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:10}}