Hi, Mark: Thanks! So I guess using adjusted p value to cut off the significant events will be a better choice than using B values?
Sabrina On Jan 11, 12:19 am, Mark Robinson <[email protected]> wrote: > Hi Sabrina. > > This is really a limma question, not an aroma.affymetrix one, but I'll > take a quick stab. Basically, you'll notice that regardless of the > value you set for 'p', you'll get the same t-statistics and p-values. > It only changes the B values (posterior log odds). > > Cheers, > Mark > > On 9-Jan-10, at 1:14 AM, sabrina wrote: > > > > > Hi, all: > > A quick question. I know after we extract frima score, I should use > > eBayes to do the following: > > > assume we have design matrix and contrast matrix, > > fit<-lmFit(exFirma,design) > > fit2<-contrasts.fit(fit,cont.matrix); > > fit2<-eBayes(fit2,proportion=p); > > > the default setting for p is 0.01 that is for gene expression. Is 0.01 > > also a good guess for this firma score purpose? Or should I use 0.001 > > or some other values? Thanks! > > > Sabrina > > -- > > When reporting problems on aroma.affymetrix, make sure 1) to run the > > latest version of the package, 2) to report the output of > > sessionInfo() and traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google > > Groups "aroma.affymetrix" group. > > To post to this group, send email to [email protected] > > To unsubscribe from this group, send email to > > [email protected] > > For more options, visit this group > > athttp://groups.google.com/group/aroma-affymetrix?hl=en > > ------------------------------ > Mark Robinson, PhD (Melb) > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: [email protected] > e: [email protected] > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > ------------------------------ > > ______________________________________________________________________ > The information in this email is confidential and intended solely for the > addressee. > You must not disclose, forward, print or use it without the permission of the > sender. > ______________________________________________________________________
-- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
