Hi,

Is it possible to do multiple group level analysis?

T1(6replication)

T2(6replication) 

T3(6replication)

T4(6replication)

I tried it but I could only see T6 vs T1. How can I check the other comparisons?

```{r DEseq2_analysis_t1_ld, include=FALSE}
ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=INDIR, design=~treatment)
dds<-DESeq(ddsHTSeq)
ddsNozero  <-  which(!mcols(dds)$allZero)
dds  <- dds[ddsNozero]
res<-results(dds)
res<-res[order(res$padj),]
```

> res
log2 fold change (MAP): treatment T6 vs T1 
Wald test p-value: treatment T6 vs T1 
DataFrame with 49044 rows and 6 columns

Thank you for the help.

J.

res2<-results(dds, contrast=c("treatment","T1", "T2"), test="Wald")

res3<-results(dds, contrast=c("treatment","T1", "T3"), test="Wald")

...

Thank you so much. 

@Michael, is that because test="Wald" is the default?