Question: removing outliers before running DESeq2
0
gravatar for nazaninhoseinkhan
13 months ago by
Iran, Islamic Republic Of
nazaninhoseinkhan370 wrote:

Dear all,

After running DESeq2 program successfully I found out that I had to detect and remove outliers from my htseq count datasets before running DESeq2. However, I am a little confused about how to perform this task.

Can u advise me the most straightforward way to do this?

Thank u in advance

Nazanin Hosseinkhan

rna-seq outliers deseq2 • 561 views
ADD COMMENTlink modified 13 months ago by arup1.7k • written 13 months ago by nazaninhoseinkhan370
1

Why do you think you need to remove outliers? I tend to remove the genes that doesnt have more than 5 counts on average across all samples but nothing more.

ADD REPLYlink written 13 months ago by firatuyulur280

Thank u so much. Yes, I've already removed genes with lower than 10 reads

ADD REPLYlink written 13 months ago by nazaninhoseinkhan370

Why 10? Why not any other?

ADD REPLYlink written 13 months ago by Arindam Ghosh170
2
gravatar for arup
13 months ago by
arup1.7k
India
arup1.7k wrote:

There is no need to remove out layers but it's better to remove the technical artifacts(noise incorporated by the sequencer). Genes/transcripts having read count within 0-10 rage is generally considered as artifacts(if the expression pattern is inconstant throughout all the samples). For more details check the following thread.

https://support.bioconductor.org/p/95755/

ADD COMMENTlink written 13 months ago by arup1.7k

Thanks a lot for your advice.

ADD REPLYlink written 13 months ago by nazaninhoseinkhan370
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