Question

Diffbind analysis warning

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Entering edit mode

mforoo1 • 0

@mforoo1-10771

Last seen 7.3 years ago

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 â€˜H3K4me3_analysisâ€™ 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

rory stark • 1.3k views

ADD COMMENT • link 7.9 years ago • updated 7.5 years ago mforoo1 • 0

score 0 · Answer 1 · 2017-02-08

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Entering edit mode

Rory Stark ★ 5.2k

@rory-stark-5741

Last seen 29 days ago

Cambridge, UK

The data() command is used to load a dataset. H3K4me3_analysis is not a pre-defined dataset so can not be loaded. What are you trying to do in the fourth-from-last line of code?

data(H3K4me3_analysis)

-R

ADD COMMENT • link 7.8 years ago Rory Stark ★ 5.2k

score 0 · Answer 2 · 2017-06-05

I could not remember why I put data(H3K4me3_analysis).

now I have another problem, I tried to use DESEQ2 method for dba.analyze. but it gave me 0 sites and also the error.

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, DBA_DESEQ2)
H3K4me3
plot(H3K4me3, contrast=1)

1 Contrast:
Group1 Members1 Group2 Members2 DB.DESeq2
1 C 3 P 3 0
Error in pv.DBAreport(pv, contrast = contrast, method = method, th = th, :
edgeR analysis has not been run for this contrast
Calls: plot ... plot.DBA -> dba.plotHeatmap -> pv.getPlotData -> pv.DBAreport
Execution halted