Question: Differentially Expressed miRNA analysis : DEseq VS. Cuffdiff
0
gravatar for illinois.ks
3.7 years ago by
illinois.ks140
Korea, Republic Of
illinois.ks140 wrote:

Hello, 

I am trying to identify differentially expressed microRNAs from my NGS data.

I have two conditions (control vs drug) Each condition has three replicates.

I have done the mapping procedure successfully and have done to identify differentially expressed miRNAs.. 

 

I have used three protocols.

1)  DeSeq

2) edgeR

3) Cuffdiff

Interestingly, my result report different results especially for  cuffdiff vs edgeR/DeSeq.

The result from edgeR/DeSeq looks very similar. 

Under the qvalue < 0.05 threshold, 

I have only  2 miRNAs by DESeq and 5 miRNAs by edgeR (luckily, those two miRNAs are overlapped..)  Also, when I relax the q value threshold 0.1 , those 5 miRNAs are overlapped in both DESeq and edgeR

 

However, for Cuffdiff result, I have 27 miRNAs (including Mirlet7d, Mirlet7a-1 etc.. which were not detected by DESeq or edgeR ). And among above 5 identfied DE microRNA (by edgeR/DESeq), only 4 of them are overlapped with 27 miRNAs by Cuffdiff.. Apprently, one of them are not.

 

So, I am not sure which tool I have to trust. I know different method has different strategry to detect DEG. however, I am nnot sure for my study, which one I have to trust. 

 

Could you please give some comments for this??  

 

ADD COMMENTlink modified 3.7 years ago by Devon Ryan88k • written 3.7 years ago by illinois.ks140
2
gravatar for Devon Ryan
3.7 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

You need to validate the DE miRNAs in additional samples, likely with qPCR. Then you'll know which result set is more reliable.

ADD COMMENTlink written 3.7 years ago by Devon Ryan88k

Could you please read the following posting?

 

Incosistent fold change signal : Differentially Expressed miRNA analysis : DEseq VS. Cuffdiff

ADD REPLYlink written 3.7 years ago by illinois.ks140
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 2.3.0
Traffic: 1799 users visited in the last hour