[BioC] DiffBind - sample sheet for multiple replicates and peak

[Paolo Kunderfranco]

Dear Antonio

I think that this problem was resolved in previous messagges, have a look to:

https://stat.ethz.ch/pipermail/bioconductor/2012-August/047351.htmlù

For the complete code you could browse August mailing list.

SampleID should be unique for each sample, and moreover also bam file
file should be unique, you should make a copy of all your bamReads and
bamControl
In my example, I compared 2 different peak callers in 3 cell lines:


SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
mES_H3K27me3_m,ES,H3K27,mES_H3K27me3,1,reads/H3K27me3/ES_H3K27me3_m.bed,reads/H3K27me3/ES_input_m.bed,peaks/H3K27me3_ES_M.bed
CMp_H3K27me3_m,CMN,H3K27,CMp_H3K27me3,1,reads/H3K27me3/CMN_H3K27me3_m.bed,reads/H3K27me3/CMN_input_m.bed,peaks/H3K27me3_CMN_M.bed
CMa_H3K27me3_m,CMA,H3K27,CMa_H3K27me3,1,reads/H3K27me3/CMA_H3K27me3_m.bed,reads/H3K27me3/CMA_input_m.bed,peaks/H3K27me3_CMA_M.bed
mES_H3K27me3_s,ES,H3K27,mES_H3K27me3,2,reads/H3K27me3/ES_H3K27me3_s.bed,reads/H3K27me3/ES_input_s.bed,peaks/H3K27me3_ES_S.bed
CMp_H3K27me3_s,CMN,H3K27,CMp_H3K27me3,2,reads/H3K27me3/CMN_H3K27me3_s.bed,reads/H3K27me3/CMN_input_s.bed,peaks/H3K27me3_CMN_S.bed
CMa_H3K27me3_s,CMA,H3K27,CMa_H3K27me3,2,reads/H3K27me3/CMA_H3K27me3_s.bed,reads/H3K27me3/CMA_input_s.bed,peaks/H3K27me3_CMA_S.bed


Like this it should work,

Cheers,
Paolo