samr analysis: How to interpret Median FDR/90th perc FDR=0.000000?

Question

[grd]

Hello everyone,

I am performing significance analysis of microarray (SAM) using the samr package. I have some doubts regarding the reported "Median FDR" and "90th perc FDR" values, as illustrated in the following:

samr.obj <- samr(data1,
            resp.type = "Two class unpaired",
            assay.type = "array",
            nperms=1000,
            center.arrays=TRUE,
            testStatistic = "standard",
            random.seed=42)
delta.table <- samr.compute.delta.table(samr.obj)
print(delta.table[,1:6])

An excerpt of delta.table:

    delta # med false pos 90th perc false pos # called median FDR 90th perc FDR
[22,] 0.869597977       1.0666667            2.400000       31 0.03440860    0.07741935
[23,] 0.954388709       0.8000000            2.133333       30 0.02666667    0.07111111
[24,] 1.043123196       0.2666667            1.333333       25 0.01066667    0.05333333
[25,] 1.135801439       0.0000000            0.000000        6 0.00000000    0.00000000

My question:

How to interpret line [25, ] having "Median FDR"= 0.000000 and "90th perc FDR"= 0.000000? Is the corrected p-value "so small" it is actually rounded?

I apologize if the question is trivial: as a young bioinformatics practitioner, I tried to look for an answer but didn't find elsewhere. Thanks.

[Pierre Lindenbaum]

Hello grd!

It appears that your post has been cross-posted to another site: https://stackoverflow.com/questions/60728054/

This is typically not recommended as it runs the risk of annoying people in both communities.

[grd]

Thank you for pointing it out, Pierre.