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".
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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
