Entering edit mode
John Antonydas Gaspar
▴
130
@john-antonydas-gaspar-3144
Last seen 9.6 years ago
Dear Bioc,
I have 5 groups of samples with their WT type, Diff type and Diff &
pure
type. To make it clear
aES,aDiff,aDiff_pure, bES,bDiff,bDiff_pure, cES,aDiff,cDiff_pure,
dES,dDiff,dDiff_pure, eES,eDiff,eDiff_pure.
I wish to do two way anova (differentiation and pure_treatment)
calculation.
Therefore I just try with the following code with limma package:
-----
Diff<-factor(c(1,1,1,2,2,2,2,2,2,1,1,1,2,2,2,2,2,2,1,1,1,2,2,2,2,2,2,1
,1,1,2,2,2,2,2,2,1,1,1,2,2,2,2,2,2))
Cond<-factor(c(1,1,1,1,1,1,2,2,2,1,1,1,1,1,1,2,2,2,1,1,1,1,1,1,2,2,2,1
,1,1,1,1,1,2,2,2,1,1,1,1,1,1,2,2,2))
design<-model.matrix(~Diff+Cond)
fit<-lmFit(limma_data,design)
fit<-eBayes(fit)
limma_deg_result<-topTableF(fit,number=45101,genelist=fit$genes,adjust
.method="BH")
limma_deg_result <-
limma_deg_result[limma_deg_result$adj.P.Val<=0.05,]
write.table(limma_deg_result, "DEgenes.txt", quote=FALSE,
row.names=FALSE, sep="\t")
-------
Of course, I ended up with a DEgenes.txt table.
However my worry is to know whether am I right in setting design.
and another thing is I wish to have the interaction effect of Diff and
Cond.
In that case in what way I have to set model in design.
I may be a fool to do this with insufficient knowledge I have to have
the interaction effect by setting design as it follows
design<-model.matrix(~Diff*Cond)
I am ended up with the following problem:
/Coefficients not estimable: Diff2:Cond2
Warning message:
Partial NA coefficients for 45101 probe(s)/
Please correct me where I do mistake.
Thanking you in advance,
antony
