Hi All,

Thanks for the reply, I could pull out the the whole information for
differentially expressed genes. The criteria used was adjust="fdr", p=0.05.
I came up with ~ 20,000 genes to be differentially expressed.

Since I wanted to analyze these genes for deregulated pathways I had to
come up with fold change values for further analysis.

I assume that for each gene FC= FCmean(test)-FCmean(blank). LogFC is log2
of FC values.

When I convert the FC values (test/blank) to foldchanges using IF function
I get lesser number of genes to be deregulated. The criteria was =>2
foldchanges and =<-2 fold changes.

My question is am I doing it right? Why does the number drastically reduce?
Is there a way to do it?

Thanks, Roopa




On Thu, Jan 31, 2013 at 5:36 AM, Maciej Jończyk <mjonczyk@biol.uw.edu.pl>wrote:

> Hi Roopa,
>
>
> results <- decideTests(fit2, adjust="fdr", p=0.05)
>> summary(results)
>> write.table(results,file="**myresults.txt")
>>
>> The results table shows ~10,000 genes to be upregulated and ~12,000 genes
>> to be down regulated.
>>
>> My question is how can I get fold change values associated with these
>> genes
>> in the results file?
>>
>
> You can create object with needed columns binded:
>
> e.g.
>
> x=cbind(fit$coefficients,fit$**p.value,p.adjust(fit$p.value,"**
> BH"),separate)
>
> Where "fit" is the result of lmFit and then eBayes commands - it contains
> "coefficients" column with (mean) log2 fold change for each gene.
>
> *In fact it haven't been clear for me at first - but I compared it to the
> output of topTable (logFC column) and it is equal.*
>
> Back to the table - proposed example will give you:
> log2 fold change,
> raw p-value,
> corrected p-value (here Benjamini-Hochberg, equall to "fdr"),
> and finally change direction for significant genes (where separate is
> result of decideTests)
>
> Before "write.table" you can change column names with colnames(x)=c(...)
>
>
> HTH
>
> --
> Maciej Jonczyk,
> Department of Plant Molecular Ecophysiology
> Faculty of Biology, University of Warsaw
> 02-096 Warsaw, Miecznikowa 1
> Poland
>
>
> --
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>

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