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[DESeq] versions, conds definition, estimateDispersions vs estimateVarianceFunctions Azazel Bioinformatics 5 11-17-2011 10:51 AM

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Old 01-15-2013, 01:17 AM   #1
jppichon
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Location: France

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Default estimateVarianceFunctions

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
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Old 01-15-2013, 11:41 PM   #2
Simon Anders
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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.
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Old 06-21-2013, 09:59 PM   #3
Baoqing
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Default 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!
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Old 06-22-2013, 04:55 AM   #4
Simon Anders
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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.
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