[BioC] limma advice required. Investigating the amplification of small sample RNA
smyth at wehi.EDU.AU
Wed Jul 26 12:16:54 CEST 2006
>Date: Wed, 26 Jul 2006 08:20:17 +0100
>From: Andrew Mcdonagh <a.mcdonagh at imperial.ac.uk>
>Subject: [BioC] limma advice required. Investigating the amplification
> of small sample RNA
>To: bioconductor at stat.math.ethz.ch
> 1) How do I carry out the t-test on a per-gene basis given the mean
>protocol effect available from the fit object. I can see that the limma
>guide has a way of obtaining the t-statistics but I'm not really sure
>how to do the test on a per gene basis. I guess it's typical
See the Limma User's Guide section 10.1, or see ?eBayes, or type
example(eBayes) at the R prompt.
> 2) I look at the stdev.unscaled and it is the same for each protocol. Is
>this to be expected? Sorry, my stats knowledge is not great.
> round_1 round_2 non_amp
>0.7071068 0.7071068 0.7071068
Yes it is to be expected. (Your experiment is symmetric in the three
protocols, so how could it be otherwise?)
> 3) What is the difference between sigma and stdev.unscaled?
See the limma chapter in the Bioconductor book for a full
explanation. sigma is just the residual standard deviation.
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