[BioC] baySeq

[Tom Hardcastle]

Hi Tina,

The easiest way to do this would be to add an additional line;
TopCountP[TopCountP$FDR < 0.01,]

There's nothing built into the topCounts function, or elsewhere, that 
gives you the table with this cutoff built in - it's a useful 
suggestion, though, and should probably be added to the next release.

Thanks,

Tom

On 08/02/2012 01:38, Tina Asante Boahene wrote:
> 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