Interprentation of appropriate statistical test
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svlachavas ▴ 780
@svlachavas-7225
Last seen 7 weeks ago
Germany/Heidelberg/German Cancer Resear…

Dear Bioconductor Community,

i would like to ask if anyone knows or has evaluated if there is any significant difference in the use of the package siggenes in r instead of the samr package, or they show similar results with regard to the appropriate parameters ? 

samr SAM siggenes bioconductor differential gene expression • 757 views
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Isn't this the same question you asked a couple of weeks ago? See Implementation of SAM statistical technique in R

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Yes it is a similar question because i didnt have a clear answer if there was a crusial difference for the two packages regarding the DE expression

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@james-w-macdonald-5106
Last seen 1 day ago
United States

The siggenes package was developed prior to samr, with the intent that it would replicate the SAM procedure which was at that time only available as an Excel plugin. Given that both siggenes and samr are intended to replicate the results that you would get from the Excel plugin, there may be slight differences between the output from the two packages, but not likely enough to materially affect the results.

That said, you have some data and can use both packages. If you are truly interested, why don't you figure this out for yourself? If I were you, I would want to do my own testing rather than relying on what some random person on the intertubes says.

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svlachavas ▴ 780
@svlachavas-7225
Last seen 7 weeks ago
Germany/Heidelberg/German Cancer Resear…

Ok thank you i would definetly check both pacages for the output of DE expression

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