voom : mean variance trend plot, How to interpret the plot

Question

[David_emir]

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

Answer 1

[Zhilong Jia]

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.

ref: http://www.genomebiology.com/2014/15/2/R29/figure/F1