[BioC] ANOVA p value calculation
a.ramasamy at imperial.ac.uk
Thu Mar 12 01:42:52 CET 2009
Assumin that columns 1-3 represents the first cell line, columns 4-6
represents second cell line etc, then you can try something like
cellline <- factor( paste("type_", rep(1:17, each=3), sep="") )
apply( Data, 2, function(gene) anova(lm(gene ~ cellline))$"Pr(>F)" )
However, in the context of microarray experiements, it is far better to
use the functions in limma package.
Sean Davis wrote:
> On Wed, Mar 11, 2009 at 1:19 PM, Antony <gasparj at 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
>> I have RMA normalized dataset in tab delimited text.
>> = ".",as.is =TRUE,na.strings = "NA",
>> colClasses = NA,check.names = FALSE,strip.white = FALSE,
>> blank.lines.skip = TRUE,
>> allowEscapes = FALSE, flush = FALSE,encoding = "unknown")
>>  31528 51
>> 17 * 3 = 51 There are 17 different cell line type samples with 3 biological
>> 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,
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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