Question: Error in DiffBind input
0
gravatar for GFM
3.8 years ago by
GFM20
European Union
GFM20 wrote:

Hello,
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".

======================================

Hello,
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?

Thanks

 

 

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

locale:
 [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            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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
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