Hi Matt congrats on the new publication.. Unfortunately I am not able to run using 10, 20 arrays. The errors this time are more consistent. Let me upload a subset of this data and send the information to you offline. Cheers! -Abhi Instantiate CNSet container.Initializing container for genotyping and copy number estimationProcessing sample stratum 1 of 1Loading chip annotation information.Loading reference normalization information.Quantile normalizing 11 arrays, one at a time. |===================================================================== ======| 100%Loading snp annotation and mixture model parameters.Calibrating 11 arrays. |==================== | 27%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 6755_8116121057_R03C01_Grn.idat and 6755_8116121057_R03C01_Red.idat2: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames = arrayNames[sel], : Chips are not of the same type. Skipping 6467_8116121013_R03C01_Grn.idat and 6467_8116121013_R03C01_Red.idat3: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames = arrayNames[sel], : Chips are not of the same type. Skipping 6476_8116121009_R02C01_Grn.idat and 6476_8116121009_R02C01_Red.idat4: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames = arrayNames[sel], : Chips are not of the same type. Skipping 6485_8116121009_R01C01_Grn.idat and 6485_8116121009_R01C01_Red.idat On Fri, Jun 6, 2014 at 12:10 PM, Abhishek Pratap <apratap@sagebase.org> wrote: > 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 <mritchie@wehi.edu.au> > 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" <apratap@sagebase.org> >> *To: *"Matt Ritchie" <mritchie@wehi.edu.au> >> *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 <apratap@sagebase.org> >> 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 <mritchie@wehi.edu.au> >>> wrote: >>> >>>> Dear Abhi, >>>> >>>> Can you provide your sessionInfo()? >>>> >>>> Thanks, >>>> >>>> Matt >>>> ------------------------------ >>>> *From: *"Abhishek Pratap" <apratap@sagebase.org> >>>> *To: *"Matt Ritchie" <mritchie@wehi.edu.au> >>>> *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 <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/crlm m/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$Sample_Group[1:5], >>>>> + cdfName = "humanomni5quadv1b", >>>>> + call.method = "krlmm", >>>>> + verbose=T >>>>> + ) >>>>> Instantiate CNSet container. >>>>> Initializing container for genotyping and copy number estimation >>>>> reading >>>>> /work/DAT_118__AML/Analysis/dset1/CNV/data/5396_6298080101_R02C0 1_Grn.idat >>>>> reading >>>>> /work/DAT_118__AML/Analysis/dset1/CNV/data/5405_6298080103_R03C0 1_Grn.idat >>>>> reading >>>>> /work/DAT_118__AML/Analysis/dset1/CNV/data/5414_6298098003_R04C0 1_Grn.idat >>>>> reading >>>>> /work/DAT_118__AML/Analysis/dset1/CNV/data/6431_8116121004_R03C0 1_Grn.idat >>>>> reading >>>>> /work/DAT_118__AML/Analysis/dset1/CNV/data/5423_6762372017_R01C0 1_Grn.idat >>>>> Processing sample stratum 1 of 1 >>>>> >>>>> Loading chip annotation information. >>>>> Loading reference normalization information. >>>>> Quantile normalizing 5 arrays, one at a time. >>>>> >>>>> |=============================================================== ================================| >>>>> 100% >>>>> Loading snp annotation and mixture model parameters. >>>>> Calibrating 5 arrays. >>>>> |========================================================= >>>>> | 60% >>>>> Error in quantile.default(M, c(1, 5)/6, names = FALSE) : >>>>> missing values and NaN's not allowed if 'na.rm' is FALSE >>>>> >>>>> In addition: Warning messages: >>>>> 1: In getProtocolData.Illumina(grnidats, sep = sep, fileExt = >>>>> fileExt$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 intended solely for the >> addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________________________________________________ >> > > [[alternative HTML version deleted]]