[BioC] analysis with no replication

Daofeng Li lidaof at gmail.com
Wed Jun 13 03:45:03 CEST 2007

Hi Richard,

Thank you for your response.
i am reading the manual of puma and will try do some analysis with puma



On 6/12/07, Richard Pearson <richard.pearson at postgrad.manchester.ac.uk> wrote:
> Li
> I'm not sure if I've understand you fully but if you are wanting to
> identify differentially expressed genes from unreplicated GeneChip data
> you have a couple of options that I am aware of:
> 1. The puma package can be used to determine uncertainties in expression
> levels which can then be used to determine probabilities of differential
> expression in a principled way. I've not included an unreplicated
> example in the puma vignette, but this is quite straightforward to do so
> give me a shout if you'd like to do this with puma but can't figure out
> how. I believe the bgx package can also do something similar.
> 2. You could simply apply your favourite summary method, and then use
> fold change between conditions to determine differentially expressed genes.
> Having said the above, with unreplicated data you have no information on
> biological variability, so the ideal approach would be to repeat the
> experiment if at all possible.
> Hope that helps
> Richard.
> Daofeng Li wrote:
> > Hi all,
> >
> > i am doing a Medicago GeneChip with six treated time points without
> > any replication
> > i used limma to analysis that,but the statistic part of Bayesian is
> > not avialable in my condition.
> > and i wanna got the expression curve of each probeset by the time
> > point and select my interested gene with always up regulated for
> > example.Could anyone give some advice on how to do analysis on my
> > condition? for i am really confused.
> >
> > Thank you
> >
> >

Daofeng Li

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