[BioC] limma

[João Fadista]

Thanks a lot for all the reply messages. 

Best regards,
João Fadista 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Marcus Davy
Sent: 27 November 2006 23:39
To: Naomi Altman; sdavis2 at mail.nih.gov; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] limma


It would be better to replace the unwanted elements with NA's rather than subset the structure, imageplot's for example will not work if the subsetted RGList or MAList is incomplete.

e.g.

MA$M[select,] <- NA


Marcus


On 11/28/06 6:19 AM, "Naomi Altman" <naomi at stat.psu.edu> wrote:

> I usually do this using an indicator function.
>
> e.g.
> select=(eBayes.out$coef[,1]>1)               #
> selects genes for which the first coef is bigger than 1
>
> MA[select,]                 # is the set of genes for which select=T
> MA[!select,]                # is the set of genes for which select=F
>
> --Naomi
>
>
> At 11:42 AM 11/27/2006, Sean Davis wrote:
>> On Monday 27 November 2006 11:28, João Fadista
>> wrote: > Dear all, > > Does anybody know how can I remove values from 
>> an MAList? > I want to remove some values from a column in MA$genes 
>> dataframe, and > consequently remove those rows from MA$genes and 
>> MA$M. Subsetting works fine with MAList objects, I think.  To remove 
>> the first five genes, you would do something like:
>> MA[-c(1:5),] To remove the first five samples, you could do something 
>> like: MA[,-c(1:5)] In other words, rows are genes and columns are 
>> samples. Sean _______________________________________________
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