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P-values returned from siggenes's sam() function

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Holger Schwender ▴ 900

@holger-schwender-344

Last seen 10.3 years ago

If you are okay with the assumption that all genes follow the same null disrtibution (and I guess so, as you are using sam), then yes. In fact, these raw p-values are used to compute the q-values (result at q.value), i.e. FDR adjusted p-values. Holger -------- Original-Nachricht -------- > Datum: Thu, 30 Apr 2009 13:45:25 -0400 > Von: Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca=""> > An: bioconductor at stat.math.ethz.ch > CC: Holger Schwender <holger.schw at="" gmx.de=""> > Betreff: P-values returned from siggenes\'s sam() function > Hi everyone, > > I have a fairly technical question. We are calling the sam() function > from packages siggenes: > result <- sam( ...... ) > and then getting the p-values like this: > result at p.value > > The Help for function sam() says that these are "raw, unadjusted p-values > of the genes". > > Does it mean an FDR function such as mt.rawp2adjp() from multtest can be > safely used on these values? > > Best, > Michal Blazejczyk > FlexArray Lead Developer --

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ADD COMMENT • link updated 15.7 years ago by Michal Blazejczyk ▴ 320 • written 15.7 years ago by Holger Schwender ▴ 900

score 0 · Answer 1 · 2009-05-04

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Michal Blazejczyk ▴ 320

@michal-blazejczyk-2231

Last seen 10.3 years ago

Hi Holger, Thank you for the answer! I've got one more small question: is the FDR algorithm used in SAM like one of the commonly known DFS's (Bonferroni, Benjamini-Hochberg, Sidak), or is it a special FDR developed for SAM? Best regards, Michal Blazejczyk Holger Schwender <holger.schw at="" gmx.de=""> wrote: > If you are okay with the assumption that all genes follow the same null > distribution (and I guess so, as you are using sam), then yes. > In fact, these raw p-values are used to compute the q-values > (result at q.value), i.e. FDR adjusted p-values. > Holger > -------- Original-Nachricht -------- >> Datum: Thu, 30 Apr 2009 13:45:25 -0400 >> Von: Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca=""> >> An: bioconductor at stat.math.ethz.ch >> CC: Holger Schwender <holger.schw at="" gmx.de=""> >> Betreff: P-values returned from siggenes\'s sam() function >> Hi everyone, >> >> I have a fairly technical question. We are calling the sam() function >> from packages siggenes: >> result <- sam( ...... ) >> and then getting the p-values like this: >> result at p.value >> >> The Help for function sam() says that these are "raw, unadjusted p-values >> of the genes". >> >> Does it mean an FDR function such as mt.rawp2adjp() from multtest can be >> safely used on these values? >> >> Best, >> Michal Blazejczyk >> FlexArray Lead Developer

ADD COMMENT • link 15.7 years ago Michal Blazejczyk ▴ 320

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Hi Michal, it is the q-value as defined by John Storey. And the values of q-values will be the same as the ones from John's package qvalue if there are no tied raw p-values. If there are ties, then the values might slightly differ because of a slightly different handling of tied p-values. Best, Holger -------- Original-Nachricht -------- > Datum: Mon, 4 May 2009 12:41:02 -0400 > Von: Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca=""> > An: Holger Schwender <holger.schw at="" gmx.de=""> > CC: bioconductor at stat.math.ethz.ch > Betreff: Re: P-values returned from siggenes\'s sam() function > Hi Holger, > > Thank you for the answer! > > I've got one more small question: is the FDR algorithm used in SAM > like one of the commonly known DFS's (Bonferroni, Benjamini- Hochberg, > Sidak), or is it a special FDR developed for SAM? > > Best regards, > Michal Blazejczyk > > > > Holger Schwender <holger.schw at="" gmx.de=""> wrote: > > If you are okay with the assumption that all genes follow the same null > > distribution (and I guess so, as you are using sam), then yes. > > > In fact, these raw p-values are used to compute the q-values > > (result at q.value), i.e. FDR adjusted p-values. > > > Holger > > > -------- Original-Nachricht -------- > >> Datum: Thu, 30 Apr 2009 13:45:25 -0400 > >> Von: Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca=""> > >> An: bioconductor at stat.math.ethz.ch > >> CC: Holger Schwender <holger.schw at="" gmx.de=""> > >> Betreff: P-values returned from siggenes\'s sam() function > > >> Hi everyone, > >> > >> I have a fairly technical question. We are calling the sam() function > >> from packages siggenes: > >> result <- sam( ...... ) > >> and then getting the p-values like this: > >> result at p.value > >> > >> The Help for function sam() says that these are "raw, unadjusted > p-values > >> of the genes". > >> > >> Does it mean an FDR function such as mt.rawp2adjp() from multtest can > be > >> safely used on these values? > >> > >> Best, > >> Michal Blazejczyk > >> FlexArray Lead Developer > --

ADD REPLY • link 15.7 years ago Holger Schwender ▴ 900