need help with Diffbind multiple groups
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Entering edit mode
Dinesh • 0
@38d1b4a3
Last seen 3 days ago
United States

Hi All,

I would like to find differential binding between H3K27 C vs K and H3K4 C vs K

19R_H3K27 20L_H3K27 20R_H3K27 (C)

16N_H3K27 18L_H3K27 18R_H3K27 (K)

19N_H3K4 19R_H3K4 20L_H3K4 (C)

16N_H3K4 18L_H3K4 18R_H3K4 (K)


dbObj_count_summits_false <-  dba.normalize(dbObj_count_summits_false,normalize="TMM",method=DBA_EDGER)

dbObj_count_summits_false$contrasts=NULL
group1_indices <- which(dbObj_count_summits_false$samples$SampleID %in% c("19R_H3K27", "20L_H3K27","20R_H3K27"))
group2_indices <- which(dbObj_count_summits_false$samples$SampleID %in% c("16N_H3K27", "18L_H3K27","18R_H3K27"))

# Apply contrast
H3K27 <- dba.contrast(dbObj_count_summits_false, group1=group1_indices, group2=group2_indices, name1="Control_H3K27", name2="Knockdown_H3K27")
H3K27 <- dba.analyze(H3K27, method=DBA_EDGER)
dba.show(H3K27, bContrasts=TRUE)

Is my contrast statement correct and is there a way to record the comparsion? Thank you! Rory Stark

DiffBind ChIPSeqData • 110 views
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