Hi Qicheng.

An FDR can be calculated from the null distribution, but the software doesn't 
do it. For example, see:


The code below may give a useful plot, basically the MUF scores for the 
dataset, with boxplots of the null distributions overlaid:

matplot( jitter(fg$nProbe), abs(fg$mufScores), pch=19, cex=.2, 
         xlim=c(7,80), xlab="Number of Probes", ylab="MUF scores", xaxt="n")
boxplot( fg$nullDistributions, at=1:length(fg$nullDistributions), add=TRUE, 
         boxwex=.4, outline=FALSE, names=NULL, las=2, yaxt="n", col="orange" )


On 2010-08-12, at 12:39 AM, Qicheng Ma wrote:

> Hi,
>          I looked at the results, fg, 
> > names(fg)
> [1] "mufScores"         "firmaGeneScores"   "nProbe"
> [4] "nullDistributions" "nProbeNull"        "plmObject"
> [7] "cls"
>            There is no Pvalue (or Qvalue),  but the paper says:
> "To alleviate this, we repeatedly sample J probes from
> the empirical distribution of all standardized residuals
> and calculated the MUF score, giving a null distribution of
> MUF scores for J probes. A false discovery rate can be calculated
> for the discoveries above a given quantile of the
> null distributions."
>               How can I get the Qvalue from false discovery rate ?
> Thanks,
> Qicheng 

Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852

The information in this email is confidential and intended solely for the 
You must not disclose, forward, print or use it without the permission of the 

When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.

You received this message because you are subscribed to the Google Groups 
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/

Reply via email to