ordinary t from limma [was: How would I normally compare swirl?]
1
0
Entering edit mode
@gordon-smyth
Last seen 7 hours ago
WEHI, Melbourne, Australia

It is easy to extract ordinary t-statistics from limma, as well as the moderated t-statistics. It is explained in Section 8.1 of the User's Guide -- do a text search for "ordinary.t". The method is

fit <- lmFit( data, design )
ordinary.t <- fit$coef / fit$stdev.unscaled / fit$sigma

Gordon

PS. I have no intention of providing the ordinary t statistic automatically, because it has such poor performance. So if you want it, you have to type one simple line of code.

>michael watson (IAH-C) michael.watson at bbsrc.ac.uk >Wed Jun 2 15:26:23 CEST 2004 > > >Hi > >I have a dataset which is pretty much IDENTICAL to the swirl dataset: > >Experiment 1 - two replicate arrays with a dye swap: > >TreatedCy5 vs UntreatedCy3 >UntreatedCy5 vs TreatedCy3 > >Experiment 2 - two replicate arrays with a dye swap: > >TreatedCy5 vs UntreatedCy3 >UntreatedCy5 vs TreatedCy3 > >This is fantastic because I can basically just copy and paste the >instructions from the limma userguide.pdf document to get my >differentially expressed genes. > >However, I want to do a comparison of limma with a "normal" method of >analysis - say a t-test. How would I carry out a t-test on this kind of >data? > >For example, the top gene limma pulls out has these values for my four >arrays for log2(Cy5/Cy3): > >-2.7, 2.7, -2.7, 3 > >This makes sense as the experiment contains a dye-swap, so if I flip my >log(ratios) such that I am always comparing treated/untreated, my values >are -2.7, -2.7, -2.7 and -3. BUT how would I go about doing a t-test on >this kind of comparison??? (I know there are huge arguments against >doing such a thing, but humour me). I mean, I basically have four >values for the same thing (the relative expression of treated against >untreated) and if I was doing a t-test - what am I comparing the values against? > >Thanks in advance > >Mick
GO limma Bioconductor • 1.0k views
ADD COMMENT
1
Entering edit mode
@gordon-smyth
Last seen 7 hours ago
WEHI, Melbourne, Australia

It is easy to extract ordinary t-statistics from limma, as well as the moderated t-statistics. It is explained in Section 8.1 of the User's Guide -- do a text search for "ordinary.t". The method is

fit <- lmFit( data, design )
ordinary.t <- fit$coef / fit$stdev.unscaled / fit$sigma

Gordon

PS. I have no intention of providing the ordinary t statistic automatically, because it has such poor performance. So if you want it, you have to type one simple line of code.

>michael watson (IAH-C) michael.watson at bbsrc.ac.uk >Wed Jun 2 15:26:23 CEST 2004 > > >Hi > >I have a dataset which is pretty much IDENTICAL to the swirl dataset: > >Experiment 1 - two replicate arrays with a dye swap: > >TreatedCy5 vs UntreatedCy3 >UntreatedCy5 vs TreatedCy3 > >Experiment 2 - two replicate arrays with a dye swap: > >TreatedCy5 vs UntreatedCy3 >UntreatedCy5 vs TreatedCy3 > >This is fantastic because I can basically just copy and paste the >instructions from the limma userguide.pdf document to get my >differentially expressed genes. > >However, I want to do a comparison of limma with a "normal" method of >analysis - say a t-test. How would I carry out a t-test on this kind of >data? > >For example, the top gene limma pulls out has these values for my four >arrays for log2(Cy5/Cy3): > >-2.7, 2.7, -2.7, 3 > >This makes sense as the experiment contains a dye-swap, so if I flip my >log(ratios) such that I am always comparing treated/untreated, my values >are -2.7, -2.7, -2.7 and -3. BUT how would I go about doing a t-test on >this kind of comparison??? (I know there are huge arguments against >doing such a thing, but humour me). I mean, I basically have four >values for the same thing (the relative expression of treated against >untreated) and if I was doing a t-test - what am I comparing the values against? > >Thanks in advance > >Mick
ADD COMMENT

Login before adding your answer.

Traffic: 676 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6