Question: Limma B statistic
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gravatar for Sabrina AT Case
8.8 years ago by
Sabrina AT Case20 wrote:
Hello, all I am using Limma for my array analysis. Based on the user's guide, I canconvert B value to probability. however, in my results, I have adj.P.Val of 0.007 with B negative. If I use the conversion, the probability will be 0.25. But when you look at the p value, it passed the significant 0.05 level. How can I explain that? Did I misunderstand some points? Thanks Sabrina
limma • 636 views
ADD COMMENTlink modified 8.8 years ago by Darlene Goldstein230 • written 8.8 years ago by Sabrina AT Case20
Answer: Limma B statistic
0
gravatar for Wolfgang Huber
8.8 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Sabrina I suspect that the question below is too vague to encourage answers. Have a look at the posting guide, and try to give a reproducible example and sessionInfo(). Best wishes Wolfgang Sabrina AT Case scripsit 17/12/10 19:59: > Hello, all > I am using Limma for my array analysis. Based on the user's guide, I > canconvert B value to probability. > however, in my results, I have adj.P.Val of 0.007 with B negative. If > I use the conversion, the probability will be 0.25. But when you look > at the p value, it passed the significant 0.05 level. How can I > explain that? Did I misunderstand some points? Thanks > > Sabrina > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENTlink written 8.8 years ago by Wolfgang Huber13k
Answer: Limma B statistic
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gravatar for Darlene Goldstein
8.8 years ago by
Darlene Goldstein230 wrote:
Sabrina AT Case <hxs61 at="" ...=""> writes: > > Hello, all > I am using Limma for my array analysis. Based on the user's guide, I > canconvert B value to probability. > however, in my results, I have adj.P.Val of 0.007 with B negative. If > I use the conversion, the probability will be 0.25. But when you look > at the p value, it passed the significant 0.05 level. How can I > explain that? Did I misunderstand some points? Thanks > > Sabrina > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > hi, It looks to me like you are confusing the p (or adj p) value with the B-stat probability. The (adj) p-value reported in the topTable function is associated with the mod-t statistic and is not related to the B-stat probability. The B-stat probability is obtained by converting the log odds ratio to obtain the probability p. Does this clear up your question? Best regards, Darlene -- Darlene Goldstein ?cole Polytechnique F?d?rale de Lausanne (EPFL) Institut de math?matiques B?timent MA, Station 8 Tel: +41 21 693 0528 CH-1015 Lausanne Fax: +41 21 693 4303 SWITZERLAND
ADD COMMENTlink written 8.8 years ago by Darlene Goldstein230
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