Question: Multiple group analysis
0
gravatar for John
3.8 years ago by
John30
John30 wrote:

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.

deseq2 • 1.2k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by John30
Answer: Multiple group analysis
2
gravatar for tony.fox2016
3.8 years ago by
tony.fox201630
tony.fox201630 wrote:

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

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

...

 

ADD COMMENTlink written 3.8 years ago by tony.fox201630
1

Yes, and in this case, you could leave off the test="Wald" (because DESeq() was run without setting test="LRT")

ADD REPLYlink written 3.8 years ago by Michael Love26k

What does LRT stand for??

ADD REPLYlink written 3.8 years ago by yoonsora0

The fastest way to learn about functions and there arguments is to check the manual pages for each function. For example:

?DESeq

or 

?results

has lots of detailed information, and on top of that you can check the vignette:

vignette("DESeq2")

ADD REPLYlink written 3.8 years ago by Michael Love26k

Thank you! It means likelihood ratio test!

ADD REPLYlink written 3.8 years ago by yoonsora0

LRT= Likelihood Ratio Test

ADD REPLYlink written 3.8 years ago by Sushant Pawar0
Answer: Multiple group analysis
0
gravatar for John
3.8 years ago by
John30
John30 wrote:

Thank you so much. 

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

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by John30
Yes
ADD REPLYlink written 3.8 years ago by Michael Love26k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 136 users visited in the last hour