voom : mean variance trend plot, How to interpret the plot
Hello All,
I am new to the Limma package and when using voom I get the following plot. I am really not sure what it means. I wonder if anyone here have seen something like this before, or could explain it to me.Is my data is good or what?
https://drive.google.com/file/d/0B4EniZCsdQJ5MFFISkVuV3liUkk/view?usp=sharing
Thanks a Lot
-Ateeq Khaliq
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David_emir
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1 answer
From the manual of limma, The limma-voom method assumes that rows with zero or very low counts have been removed. It seems that you did not filter genes with low counts.
Gene-wise means and variances of RNA-seq data are represented by black points with a LOWESS trend in the voom, mean-variance figure. Read figure in ref1.
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Zhilong Jia
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Zhilong Jia
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