Diffbind analysis warning
2
0
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 ‘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

 

 

rory stark • 1.3k views
ADD COMMENT
0
Entering edit mode
Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 5 weeks 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
0
Entering edit mode
mforoo1 • 0
@mforoo1-10771
Last seen 7.3 years ago

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

 

ADD COMMENT

Login before adding your answer.

Traffic: 503 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6