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volcano plot of up and down genes into two parts, resprctively.

When I do volcano plot of my RNA-seq data, I found the up and down genes cluster into two parts (two parts in up genes and two parts in down genes), resprctively. Can someone please explain to me why this is the case? Thanks a lot.

Volcano plot

rna-seq volcano plot
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written by Bing Dwen Dwen • Bing Dwen Dwen

strange that entitites with fc values between ~5-~10 fold changes, on either side, are missing or not statistically significant.

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written by cpad0112 cpad0112

Do you know why it happens？ some mistakes during processing of data？

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written by Bing Dwen Dwen • Bing Dwen Dwen

1 answer

These have large fold changes but rather low pvalues. If I had to guess then these are genes with many zeros. Some prefiltering of the data, e.g. edgeR::filterByExpr() can help removing unreliable calls.

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written by ATpoint ATpoint

You are right :) there are some zore data inside, so it means that are these data with zeros unavailable?

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written by Bing Dwen Dwen • Bing Dwen Dwen

What do you mean with "unavailable"?

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written by ATpoint ATpoint

Do you mean that there are a lot of zero data in the data, will these data be removed after filtering the data?

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written by Bing Dwen Dwen • Bing Dwen Dwen

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