Hi,

I am trying to use DESeq2 package. I have some question's related to that.

1. DESeq2 manual say's in MAplot function  Points will be colored red if the adjusted p value is less than 0.1. Can i change the value to 0.05. If yes how??

2. Also point which falls out of the window are plotted as open triangles. In the file what should I see in the column of adjusted p value. Will it be NA??

Thanks

Varun

1. DESeq2 manual say's in MAplot function  Points will be colored red if the adjusted p value is less than 0.1. Can i change the value to 0.05. If yes how??

In the help page you get from ?plotMA function for a DESeqDataSet, you'll see that there is an alpha parameter you can tweak which sets the significance threshold to plot.

2. Also point which falls out of the window are plotted as open triangles. In the file what should I see in the column of adjusted p value. Will it be NA??

The position on the y-axis is defined by the log fold change of the gene expression, what you'll see in the related adjusted p value column is not a function of the fold change, but rather its p-value, so there isn't a real "direct" answer to your question (although on average you'd expect high logFC's with low p-values, but it's not always the case), if you know what I mean?

You should note that NA pvalues come from two sources (if you've run DESeq2 w/o any tweaks):

1. From genes that have outlier expression in >= 1 sample; or
2. From genes that have been filtered out by the "independent filtering" mojo DESeq does by default to reduce the multipe-testing burden via removing genes that have a small chance of being differentially expressed