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Old 02-22-2017, 05:03 PM   #1
icanwinwyz
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Default Independent filtering by using fold change in DESeq2

Hi everyone,
Thanks for reading my post.

I know DESeq2 uses normalized mean count as independent filtering to improve the performance of multiple testing error correction. I would like to know is it possible I can add the criteria, |log2FC| > 1, together with normalized mean count as the independent filtering? If so, how could I add this criteria? by using "filter=" or "filterFun=" argument? How to write the command?

What I know now is to change the "lfcThreshold=" to 1, but this only change the null hypothesis from 0 to 1, not actually filter any genes.

Many Thanks in advance!
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Old 02-22-2017, 11:58 PM   #2
dpryan
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No you can't use fold-change in independent filtering, it wouldn't then be independent. You can filter genes after the fact for the fold-change threshold you want.
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Old 02-23-2017, 08:24 AM   #3
icanwinwyz
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Quote:
Originally Posted by dpryan View Post
No you can't use fold-change in independent filtering, it wouldn't then be independent. You can filter genes after the fact for the fold-change threshold you want.
Hi dpryan,
Thanks for your reply. You mean I should run DESeq for DE analysis first and then filter out the genes with small fold change? If so, could I only perform multiple testing error correction for those genes remained instead of all the genes tested? Since this would give me more significant DE genes with big fold change.

Thanks.
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Old 02-23-2017, 08:34 AM   #4
wdecoster
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But that is a violation of independent filtering principle, you cannot filter for something you are testing for. Obviously it is great for your p-values, but also completely invalid and should be considered p-value-hacking.
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Old 02-23-2017, 08:51 AM   #5
icanwinwyz
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Quote:
Originally Posted by wdecoster View Post
But that is a violation of independent filtering principle, you cannot filter for something you are testing for. Obviously it is great for your p-values, but also completely invalid and should be considered p-value-hacking.
Hi wdecoster,
Thanks for you reply.
So nothing we can do by using fold change to filter the genes? any suggestion? Thanks
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Old 02-23-2017, 10:12 AM   #6
dpryan
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You can filter genes by fold-change after calculating p-values and adjusting for multiple testing. If you do anything like that beforehand odds are good that you'll end up with me as a reviewer and I will guarantee that your paper is rejected.
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