Question: rnaseqDTU DTU workflow - pots-hoc Filter
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gravatar for fiona.dick91
6 months ago by
fiona.dick9110
fiona.dick9110 wrote:

Hi,

I have been following the DTU workflow which is linked to the package rnaseqDTU and the paper: "Swimming downstream: statistical analysis of differential transcript usage following Salmon" https://f1000research.com/articles/7-952/v3

It is mentioned that, in favor of controlling the FDR of DRIMSeq one should apply a post-Hoc filter to exclude "transcripts with small SD of the per-sample proportions". This was not suggested to be done for results of DEXSeq and its workflow which is described in the same paper. The reason is that DEXSeq seemed to "be closer to controlling its FDR".

I wonder if this post-Hoc filter would be redundant if one is only interested in the intersection of DRIMSeq and DEXSeq results. As those FPs that were called by DRIMSeq would in the best case not be present in DEXSeq. (Having in mind that the intersection of results from both tools might lack some DTUs that were found by DRIMseq being more sensitve).

Thanks in advance

Fiona

drimseq dtu rnaseqdtu • 199 views
ADD COMMENTlink modified 6 months ago by Michael Love24k • written 6 months ago by fiona.dick9110
Answer: rnaseqDTU DTU workflow - pots-hoc Filter
2
gravatar for Michael Love
6 months ago by
Michael Love24k
United States
Michael Love24k wrote:

I suppose that you could skip the filter then. The filter is just a suggestion (and I should said that it's only coming from my benchmark, not from the package authors). I think of it as analogous to post-hoc filtering of genes with small LFC. This is common practice and easy to do, although in theory the minimum effect size could also be incorporated into the testing procedure somehow (e.g. TREAT and lfcThreshold in edgeR/limma and DESeq2 respectively).

ADD COMMENTlink modified 6 months ago • written 6 months ago by Michael Love24k

Thanks for the answer and sorry for late answer. Is it ok to perform post-hoc filter on lfc transcripts after testing and reporting the unchanged pvalue? Is it ok to use DEXSeq::estimateExonFoldChange and DRIMSeq::coefficients for this purpose if Id want to do the same post hoc filtering on both tool results?

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by fiona.dick9110
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