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Question: Diffbind analysis warning
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gravatar for mforoo1
17 months ago by
mforoo10
mforoo10 wrote:

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

 

 

ADD COMMENTlink modified 12 months ago • written 17 months ago by mforoo10
0
gravatar for Rory Stark
16 months ago by
Rory Stark2.5k
CRUK, Cambridge, UK
Rory Stark2.5k wrote:

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 COMMENTlink modified 16 months ago • written 16 months ago by Rory Stark2.5k
0
gravatar for mforoo1
12 months ago by
mforoo10
mforoo10 wrote:

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 COMMENTlink written 12 months ago by mforoo10
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