[BioC] baySeq

[Tina Asante Boahene]

Hi all,

Is it possible to find the FDR of DE genes in baySeq at a set percentage.

Is there a function used in the baySeq vignette to find the FDR at a set percentage.

Example to find the FDR for a topCounts at say 1% within baySeq.

TopCountP<-topCounts(CDPost.Poi, number = 22490, group = 2)

This will give all the FDR for this dataset, however is there a way to just have the result with a pre-set FDR. 

Also is there something similar for the DEGseq package.

Thanks.

Kind Regards

Tina
________________________________________
From: Severin Uebbing [severin.uebbing at ebc.uu.se]
Sent: 06 February 2012 16:40
To: Tina Asante Boahene
Subject: Re: [BioC] baySeq

Hi Tina,

I'm not quite sure what you mean with your question about the plotMA
function. However, if you want to create a plot, where a subset of genes
is plotted in red, whereas the rest is plotted in black, you can
certainly do so. You could, e.g. create a vector which contains either
"red" or "black" (much like the example in the baySeq vignette), but
according to your wishes. If you want to have all differentially
expressed genes coloured red, then you might want to create a vector,
where all genes with a posterior probability of exp(DE) > 0.3 are "red".
All you need to do to get your coloured plot is to use plotMA(..., col =
my_colour_vector). Is that what you are looking for?

The second question should also be solvable. The object where you saved
your priors in, e.g. according to manual:

CDP.NBML <- getPriors.NB(...)

contains a slot called @priors with an object $priors. So if you want to
export this vector, you can do so using the command

write.table(CDP.NBML at priors$priors,file = "my_file.csv", sep = "\t",
row.names = F, quote = F)

This will create a tab delimited file which you can also open in Excel
if you like.

Out of curiosity, why are you interested in the priors? Shouldn't you
want to look at the posteriors?

Severin

On 02/06/2012 02:37 PM, Tina Asante Boahene wrote:
> Dear All,
>
> I just hoping if you would not mind help me answer these questions
>
> With regard to the plotMA I have realised that this plot was tailor to the data used my the author.
> However, is there a general way to approach this to incorporate with different dataset.
>
> plotMA.CD(CD, samplesA = c(1,3,6,8,10), samplesB = c(2,4,5,7,9), col = c(rep("red",
> 100), rep("black", 900)))
>
> Also is there a way to write the output of the priors to a spreadsheet eg Excel.
>
> Thank you.
>
>
> Kind Regards
>
> Tina
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--
Severin Uebbing
Dept. Ecology & Genetics | Evolutionary Biology
Evolutionary Biology Centre
Uppsala University
Norbyvägen 18D
SE-752 36 Uppsala, Sweden
Phone: +46-18 471 28 27