Question: removing outliers before running DESeq2
0
gravatar for nazaninhoseinkhan
8 months ago by
Iran, Islamic Republic Of
nazaninhoseinkhan360 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 • 373 views
ADD COMMENTlink modified 8 months ago by arup870 • written 8 months ago by nazaninhoseinkhan360
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 8 months ago by firatuyulur250

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

ADD REPLYlink written 8 months ago by nazaninhoseinkhan360

Why 10? Why not any other?

ADD REPLYlink written 8 months ago by Arindam Ghosh160
2
gravatar for arup
8 months ago by
arup870
India
arup870 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 8 months ago by arup870

Thanks a lot for your advice.

ADD REPLYlink written 8 months ago by nazaninhoseinkhan360
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