estimateVarianceFunctions

[jppichon]

Hi,

I tried to do the analysis of the "example.File" with DESeq 1.10.1.
The following message appeared:

Erreur : 'estimateVarianceFunctions' is defunct.
Use 'estimateDispersions' instead.
See help("Defunct")

So I tried to use "estimateDispersions". It seemed to be successful, but after running the "nbinomTest" function all padj value were equal to 1 and resVar weren't calculated.

Does someone has experimented the same?

JP

[Simon Anders]

Please always use a current version of both the package and the documentation. You seem to be reading an old version of the vignette if it still mentions 'estimateVarianceFunction'.

As for the p values, you will have to give us much more information on what you are doing before we can make any guesses.

[Baoqing]

p value is negative

Hi, Guys

I probably followed the old version as well. But after the error message, i changed to run:
cds = estimateDispersions(cds)
res = nbinomTest(cds, "T", "N") #T, N two treatments, all of my samples are single reads

When i looked at the results:

i saw p value is negative in some rows, however, the adjusted p value seems okay. Is it normal, or do i have to specify more parameters?

Thank you!

[Simon Anders]

Negative p values are impossible. You must have either uncovered a very subtle bug, or have done something wrong. Post more details if the problem persists.