Question

ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of 'dimnames' [2] not equal to array extent

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ssn4ssn • 0

@ssn4ssn-10166

Last seen 8.6 years ago

Hi all,

I am new with the analysis of chipseq and I am trying to get the quality of a chipseq sample but the chipqc results in an error.

"Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of 'dimnames' [2] not equal to array extent"

The command I used is

sample <- ChIPQCsample("sample12_sorted.bam", annotation="hg38")

What could be the possible reason for this error?

> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ChIPQC_1.6.1               DiffBind_1.16.3            RSQLite_1.0.0             
 [4] DBI_0.3.1                  locfit_1.5-9.1             GenomicAlignments_1.6.3   
 [7] Rsamtools_1.22.0           Biostrings_2.38.4          XVector_0.10.0            
[10] limma_3.26.9               SummarizedExperiment_1.0.2 Biobase_2.30.0            
[13] GenomicRanges_1.22.4       GenomeInfoDb_1.6.3         IRanges_2.4.8             
[16] S4Vectors_0.8.11           BiocGenerics_0.16.1        ggplot2_2.1.0             

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.4             lattice_0.20-33         GO.db_3.2.2             gtools_3.5.0           
 [5] digest_0.6.9            Nozzle.R1_1.1-1         plyr_1.8.3              futile.options_1.0.0   
 [9] BatchJobs_1.6           backports_1.0.2         ShortRead_1.28.0        gplots_3.0.1           
[13] zlibbioc_1.16.0         GenomicFeatures_1.22.13 annotate_1.48.0         gdata_2.17.0           
[17] Matrix_1.2-5            checkmate_1.7.4         systemPipeR_1.4.8       GOstats_2.36.0         
[21] splines_3.2.5           BiocParallel_1.4.3      chipseq_1.20.0          stringr_1.0.0          
[25] pheatmap_1.0.8          RCurl_1.95-4.8          biomaRt_2.26.1          munsell_0.4.3          
[29] sendmailR_1.2-1         rtracklayer_1.30.4      base64enc_0.1-3         BBmisc_1.9             
[33] fail_1.3                edgeR_3.12.1            XML_3.98-1.4            AnnotationForge_1.12.2 
[37] bitops_1.0-6            grid_3.2.5              RBGL_1.46.0             xtable_1.8-2           
[41] GSEABase_1.32.0         gtable_0.2.0            magrittr_1.5            scales_0.4.0           
[45] graph_1.48.0            KernSmooth_2.23-15      amap_0.8-14             stringi_1.0-1          
[49] reshape2_1.4.1          hwriter_1.3.2           genefilter_1.52.1       latticeExtra_0.6-28    
[53] futile.logger_1.4.1     brew_1.0-6              rjson_0.2.15            lambda.r_1.1.7         
[57] RColorBrewer_1.1-2      tools_3.2.5             Category_2.36.0         survival_2.39-2        
[61] AnnotationDbi_1.32.3    colorspace_1.2-6        caTools_1.17.1

Thank you.

chipseq chipqc • 1.4k views

ADD COMMENT • link updated 8.6 years ago by Thomas Carroll ▴ 420 • written 8.6 years ago by ssn4ssn • 0

score 0 · Answer 1 · 2016-04-28

hi, Sorry for the delay in replying. This looks like there is something wrong with the parsing of SAM flags. Could you can provide a subsample of your BAM file which reproduces this problem? You should be able to generate this with samtools using command below where FRACTION is fraction of BAM file to keep. "samtools view -hb -s FRACTION *sample12_sorted.bam*" or for example. "samtools view -hb -s 0.00001 *sample12_sorted.bam*" best, Tom On Fri, Apr 22, 2016 at 5:00 PM, ssn4ssn [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User ssn4ssn <https: support.bioconductor.org="" u="" 10166=""/> wrote Question: > ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) > : length of 'dimnames' [2] not equal to array extent > <https: support.bioconductor.org="" p="" 81171=""/>: > > Hi all, > > I am new with the analysis of chipseq and I am trying to get the quality > of a chipseq sample but the chipqc results in an error. > > *"Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of > 'dimnames' [2] not equal to array extent"* > > The command I used is > > *sample <- ChIPQCsample("sample12_sorted.bam", annotation="hg38")* > > What could be the possible reason for this error? > > > > Thank you. > > ------------------------------ > > Post tags: chipseq, chipqc > > You may reply via email or visit ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of 'dimnames' [2] not equal to array extent >