Question: ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of 'dimnames' [2] not equal to array extent
0
gravatar for ssn4ssn
3.6 years ago by
ssn4ssn0
ssn4ssn0 wrote:

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 • 875 views
ADD COMMENTlink modified 3.6 years ago by Thomas Carroll400 • written 3.6 years ago by ssn4ssn0
Answer: ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) :
0
gravatar for Thomas Carroll
3.6 years ago by
United States/New York/The Rockefeller University
Thomas Carroll400 wrote:
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 >
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Thomas Carroll400
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