Hi John,

That's not a huge amount of info to go on.

Is there any a priori reason for A3 to be different? Or have you just
deduced this from the boxplots? Why do you believe A3 over A2/A2 to be the
"correct result"?

I don't understand why you wish to compare A3 on it's own to B1-3. By
comparing 1 sample against 3 using t.test, as I understand it, you will be
conducting a one-sample t-test, which means you hypothesise that the A3 is
the population mean (which it most likely isn't, since it's from 1 sample,
and especially because it appears to be an outlying sample). I suspect you
might not get a reproducible result in this manner.

Also, Perhaps if the delta Cqs are all higher/lower in A3 compared to A2
and A1, something went wrong in normalisation. Perhaps check the expression
of your reference genes.

Best wishes,

Jim

On 27 February 2012 15:07, John Alexander <fbsja@leeds.ac.uk> wrote:

>
> Hi all,
> I'll try list my problem in the following below.
> Data: from RT-PCR experiment (log(2^-delta delta t) data)
> Experiment: (A1,A2,A3,B1,B2.B3) samples belonging to 2 groups (A,B) and
> want to find the differential expressed genes
> Statistical test : t-test or use limma between 2 groups. It works fine.
> Software : R [Packages: genefilter,limma]
>
> Problem: We know that A3 is slightly different from the rest of the
> samples by viewing the boxplot so I want to find the differentially
> expressed genes of A3 against the group B (B1,B2 and B3)….This means 1
> sample against a group of 3. As it is I don't have enough samples and using
> a t-test using sample A3 and mean of (B1,B2,B3) seems statistically
> incorrect for this purpose, I tried using LIMMA package thinking it should
> produce sensible results. Would this be correct or should I be using any
> other tests.
> Any help rendered is appreciated.
> cheers,
> John.
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

