Question: Error in DiffBind input
gravatar for GFM
3.8 years ago by
European Union
GFM20 wrote:

Please Ignore the below error.
I found the problem. The sample table had "raw" under the PeakCaller column, as in the example, but should be "bed".


I am trying to read data into DiffBind, and I am getting an error.

My sample file:

SampleID Patient Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller
p1_non p1 non 1 p1_non.bam p1_non_C p1_non_C.bam p1_non_peaks.bed raw
p2_non p2 non 2 p2_non.bam p2_non_C p2_non_C.bam p2_non_peaks.bed raw
p1_act p1 act 1 p1_act.bam p1_act_C p1_act_C.bam p1_act_peaks.bed raw
p2_act p2 act 2 p2_act.bam p2_act_C p2_act_C.bam p2_act_peaks.bed raw

when I try to read the input with:

my_data = dba(sampleSheet="sample_file.csv")

I get the error:
p1_non    non 1 raw
Error in peaks[, pCol]/max(peaks[, pCol]) :
  non-numeric argument to binary operator

The peaks file is a bed file from MACS2 output (5 columns).
In the sample file I had also full path for the files.

Can you help with this please?




> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] DiffBind_1.12.3           GenomicAlignments_1.2.2   Rsamtools_1.18.3          Biostrings_2.34.1         XVector_0.6.0            
 [6] limma_3.22.7              DESeq2_1.6.3              GenomicFeatures_1.18.7    AnnotationDbi_1.28.2      GenomicRanges_1.18.4     
[11] GenomeInfoDb_1.2.5        IRanges_2.0.1             S4Vectors_0.4.0           BiocInstaller_1.16.5      amap_0.8-14              
[16] ggplot2_1.0.1             matrixStats_0.14.2        gplots_2.17.0             RColorBrewer_1.1-2        Biobase_2.26.0           
[21] RcppArmadillo_0.6.500.4.0 Rcpp_0.12.3               BiocGenerics_0.12.1       methylKit_0.9.4          

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3     annotate_1.44.0     base64enc_0.1-3     BatchJobs_1.6       BBmisc_1.9          BiocParallel_1.0.3  biomaRt_2.22.0     
 [8] bitops_1.0-6        brew_1.0-6          caTools_1.17.1      checkmate_1.7.1     chron_2.3-47        cluster_2.0.3       codetools_0.2-14   
[15] colorspace_1.2-6    data.table_1.9.6    DBI_0.3.1           digest_0.6.8        edgeR_3.8.6         fail_1.3            foreach_1.4.3      
[22] foreign_0.8-66      Formula_1.2-1       gdata_2.17.0        genefilter_1.48.1   geneplotter_1.44.0  grid_3.1.1          gridExtra_2.0.0    
[29] gtable_0.1.2        gtools_3.5.0        Hmisc_3.17-0        iterators_1.0.8     KernSmooth_2.23-15  lattice_0.20-31     latticeExtra_0.6-26
[36] locfit_1.5-9.1      magrittr_1.5        MASS_7.3-40         munsell_0.4.2       nnet_7.3-11         plyr_1.8.2          proto_0.3-10       
[43] RCurl_1.95-4.7      reshape2_1.4.1      rpart_4.1-10        RSQLite_1.0.0       rtracklayer_1.26.3  scales_0.3.0        sendmailR_1.2-1    
[50] splines_3.1.1       stringi_1.0-1       stringr_1.0.0       survival_2.38-3     tools_3.1.1         XML_3.98-1.3        xtable_1.8-0       
[57] zlibbioc_1.12.0   



diffbind • 819 views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by GFM20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 212 users visited in the last hour