Question: diffbind: use of continuous variables
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gravatar for janani.sundaresan
4 months ago by
janani.sundaresan0 wrote:

How can I correct continuous variable (eg: age) in diffbind? I find that in my data age is a covariate that I need to correct for. The column TISSUE is used for AGE in my data. I tried by altering the contrast and then running dba.analyze but I get 0 peaks after blocking AGE.

library(DiffBind)
library(DESeq2)
library(edgeR)
library(GenomicAlignments)

> chip1
21 Samples, 200401 sites in matrix (367587 total):

> dba(chip1, minOverlap=2,
+     sampleSheet="/scratch/CHIP/DATA/NBB/CHIP_NBB.csv", 
+     config=data.frame(RunParallel=TRUE, reportInit="chip1", DataType=chip_DATA_GRANGES, 
+                       AnalysisMethod=chip_DESEQ2, minQCth=15, fragmentSize=125, 
+                       bCorPlot=TRUE, th=0.05, bUsePval=FALSE),
+     peakCaller="macs")
21 Samples, 200401 sites in matrix (367587 total):

> chip1 <- dba.count(chip1, summits=150)
Re-centering peaks...

> chip1 <- dba.contrast(chip1, categories=DBA_CONDITION,block = DBA_TISSUE)
> chip1 <- dba.analyze(chip1)

1 Contrast:
  Group1 Members1  Group2 Members2 Block1Val InBlock1 Block2Val InBlock2 Block3Val InBlock3 Block4Val InBlock4 Block5Val InBlock5
1   CASE       10 CONTROL       11       102        1        73        1        75        2        76        1        77        1
Block6Val InBlock6 Block7Val InBlock7 Block8Val InBlock8 Block9Val InBlock9 Block10Val InBlock10 Block11Val InBlock11 Block12Val
1        78        1        80        1        81        1        84        4         85         1         86         1         88
InBlock12 Block13Val InBlock13 Block14Val InBlock14 Block15Val InBlock15 Block16Val InBlock16 Block17Val InBlock17 DB.DESeq2
1         1         89         1         91         1         93         1         95         1         96         1      1632
DB.DESeq2.block
1               0

diffbind deseq2 • 98 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by janani.sundaresan0
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