I used RSEM to align and quantify RNAseq, then used edgeR to get differentially expressed genes with someting like the following:
library("edgeR");
d0<-read.delim("mydata.txt", row.names="gene_id");
d<-d0[c("c1","c2","t1","t2")];
attach(d);
group<-factor(c(1,1,2,2));
dgeList <- DGEList(counts=d, group=group);
normFac <- calcNormFactors(dgeList); # ERCC normalization
dsgn <- model.matrix(~group);
disp <- estimateDisp(normFac, dsgn);
qlFit <- glmQLFit(disp, dsgn);
qlfTest <- glmQLFTest(qlFit, coef=2);
topTags(qlfTest);
# do GO analysis
go <- goana(qlfTest, specifes="Hs");
The code works up to "topTags(qlfTest)", but stopped at the last line with the following error:
Error in goana.default(qlfTest, specifes = "Hs", de = list(Up = c("A1BG", :
No genes found in universe
Any ideas?
Thanks!
show us a snippet of mydata.txt
Also it should be
species = "Hs"
not specifes.Thanks for the correction. However, with "species", I got the same error.
And what's the output of
topTags(qlfTest)
?