User: ingerslev

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ingerslev0
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Posts by ingerslev

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Comment: C: Odd P-value distribution in edgeR on RRBS data
... I will play it safe and stick to your initial suggestion and only filter out sites with 100% or 0% methylation. The data is RRBS, but it is sequenced quite deeply, maybe more than necessary.  Your explanation of filterByExpr made it make sense to me - thanks. ...
written 5 months ago by ingerslev0
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Comment: C: Odd P-value distribution in edgeR on RRBS data
... This answers my question, thank you. Can I ask two more questions? Firstly, why is filterByExpr not appropriate, if it is used on the Coverage object from the f1000 paper? The function seems to be doing almost the same. Secondly, how is the model affected by removing sites that are 0% or 100% across ...
written 5 months ago by ingerslev0
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Comment: C: Odd P-value distribution in edgeR on RRBS data
... I used the filtering as in Section 4.7.3 when I wrote this question, I have now also tested the filtering used in f1000 paper and also the filterByExpr function (with the design matrix) of edgeR. The edgeR guide leaves me with 150.000 sites, f1000 with 260.000 and filterByExpr with 592.000 sites. In ...
written 5 months ago by ingerslev0
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Comment: C: Odd P-value distribution in edgeR on RRBS data
... I just realised that filtering out all sites where the average number of methylated or unmethylated reads across all samples is less than one seems to solve both problems. Now the distribution of P-values looks uniform with a slight increase in sites with a low P-value. If anyone has an explanation, ...
written 5 months ago by ingerslev0
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Odd P-value distribution in edgeR on RRBS data
... I have been running an analysis of RRBS data using edgeR, following the guide in the edgeR manual. The metadata looks like this: File Sample Condition S1_Pre.cov.gz S1 Pre S1_Post.cov.gz S1 Post ... ... ... S9_Pre.cov.gz S9 ...
edger rrbs written 5 months ago by ingerslev0 • updated 5 months ago by Gordon Smyth37k

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