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What causes Linear relations on MAplots?

Hello I am sort of a newbie in statistical science, so I hope this isn't a terrible question.

I am doing an analysis on example data, and I do the MAplot on my normalized counts from my DESeq2 results. This is what I get: MA plot with a linear relationship

So we have a normal(i think) MAplot, of my two groups, each group has 3 samples.

But in bottom left corner, that is downregulated genes with low read counts we have a linear relation between read counts and Logfold change.

What could cause this?

Are these genes valid?

Another similar phenomena is seen when you compare two samples counts(before any rlog transform): Sample differences with lines at low read counts.

At the low read counts, again we have what looks like straight lines. Does it have something to do with the low sampling rate(counts) of these genes causing aliasing?

Best regards, Gabriel

maplot rna-seq logfold change
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written by Gabriel Gabriel

1 answer

If you think in terms of algebra a line would be where y/x is a constant.

In the MA plot, Y=log(A)-log(B) and X=log(A)+log(B) so if (log(A)-log(B))/(log(A)+log(B))=constant then this is probably all the values from the gene set A that are 0 or gene set B are 0

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written by cmdcolin cmdcolin

Thank you. Your answer checks out! I used the identify() function to extract one of the gene names from the lines, and then I checked the raw data. It seems one group had all columns as 0, and the control group had all columns from 50-90 for that specific gene.

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written by Gabriel Gabriel

Please embed your images properly as suggested above ;-)

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written by ATpoint ATpoint

Sorry didn't see it until now, done.

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written by Gabriel Gabriel

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