ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of 'dimnames' [2] not equal to array extent
1
0
Entering edit mode
ssn4ssn • 0
@ssn4ssn-10166
Last seen 5.5 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 • 1.0k views
ADD COMMENT
0
Entering edit mode
@thomas-carroll-7019
Last seen 16 months ago
United States/New York/The Rockefeller …
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 COMMENT

Login before adding your answer.

Traffic: 364 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6