Hello,
I tried to do test run of Diffbind for my ChIP-seq data. I followed the manual and used the basic command. these are my command :
library(DiffBind)
setwd("/project/maheshid/mforoo1/DiffBind")
samples <- read.csv("H3K4me3.csv", header=TRUE)
names(samples)
samples
H3K4me3 <- dba(sampleSheet="H3K4me3.csv")
H3K4me3
plot(H3K4me3)
H3K4me3 <- dba.count(H3K4me3 , summits=250)
H3K4me3
plot(H3K4me3)
H3K4me3 <- dba.contrast(H3K4me3, categories=DBA_TREATMENT)
H3K4me3 <- dba.analyze(H3K4me3)
H3K4me3
plot(H3K4me3, contrast=1)
H3K4me3.DB <- dba.report(H3K4me3, th=1, bCounts=TRUE)
H3K4me3.DB
data(H3K4me3_analysis)
dba.plotMA(H3K4me3)
dba.plotPCA(H3K4me3, DBA_TREATMENT,label=DBA_ID)
dba.plotPCA(H3K4me3, contrast=1,label=DBA_ID)
every thing is fine except that i got warning for DBA_analysis.
In data(H3K4me3_analysis) : data set ‘H3K4me3_analysis’ not found
Would you please help me to understand this warning?
Many thanks
Maryam
PS. my sample sheet :
SampleID | Tissue | Factor | Condition | Treatment | Replicate | bamReads | ControlID | bamControl | Peaks | PeakCaller |
WTC1 | Shoot | H3K4me3 | WT | P+ | 1 | rep1_WT_C_H3K4me3_bowtie.bam | InPutC1 | rep1_WT_C_input_bowtie.bam | sorted_rep1_WT_C_H3K4me3_bowtie-W200-G200-FDR0.001-islandfiltered.bed | bed |
WTC2 | Shoot | H3K4me3 | WT | P+ | 2 | rep2_WT_C_H3K4me3_trimmed_bowtie.bam | InPutC2 | rep2_WT_C_input_bowtie.bam | sorted_rep2_WT_C_H3K4me3_trimmed_bowtie-W200-G200-FDR0.001-islandfiltered.bed | bed |
WTC3 | Shoot | H3K4me3 | WT | P+ | 3 | rep3_WT_C_H3K4me3_bowtie.bam | InPutC3 | rep2_WT_C_input_bowtie.bam | sorted_rep3_WT_C_H3K4me3_bowtie-W200-G200-FDR0.001-islandfiltered.bed | bed |
WTP1 | Shoot | H3K4me3 | WT | P- | 1 | rep1_WT_P_H3K4me3_bowtie.bam | InPutP1 | rep1_WT_P_input_bowtie.bam | sorted_rep1_WT_P_H3K4me3_bowtie-W200-G200-FDR0.001-islandfiltered.bed | bed |
WTP2 | Shoot | H3K4me3 | WT | P- | 2 | rep2_WT_P_H3K4me3_bowtie.bam | InPutP2 | rep2_WT_P_input_bowtie.bam | sorted_rep2_WT_P_H3K4me3_bowtie-W200-G200-FDR0.001-islandfiltered.bed | bed |
WTP3 | Shoot | H3K4me3 | WT | P- | 3 | rep3_WT_P_H3K4me3_bowtie.bam | InPutP3 | rep2_WT_P_input_bowtie.bam | sorted_rep3_WT_P_H3K4me3_bowtie-W200-G200-FDR0.001-islandfiltered.bed | bed |