On Wed, Mar 11, 2009 at 1:19 PM, Antony <gasparj@uni-koeln.de> wrote:

> Dear Sir/Madam,
>
> I wish to do ANOVA p value computation with Bioconductor.
>

You might want to look at the limma package, though there are a number of
others.


>
> I have RMA normalized dataset in tab delimited text.
>
> Data<-read.table("RMA-normalized.txt",row.names=1,sep="\t",header=TRUE,dec
> = ".",as.is =TRUE,na.strings = "NA",
>                colClasses = NA,check.names = FALSE,strip.white = FALSE,
> blank.lines.skip = TRUE,
>                allowEscapes = FALSE, flush = FALSE,encoding = "unknown")
>
> dim(Data)
> [1] 31528    51
>
> 17 * 3 = 51 There are 17 different cell line type samples with 3 biological
> replicates.
>
> I wish to do ANOVA - p value calculation for finding out the differentially
> expressed genes.
>
> Kindly help me out to use the right Bioconductor package. Using multtest
> package I tried to do F stat but could not. When I try
> the R console window goes off. Could be due to many number of couloumns?.
>

You'll probably need to read the posting guide to get a bit better help.  In
particular, you would need to provide at least your code and the output,
error messages, and sessionInfo().


>
> Please help me out to find a solution.
>
> Thanking you in advance,
>
>
> With kind regards,
> antony
>
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