[BioC] edgeR and FDR values always equals 1
a.gossner at ed.ac.uk
Fri Nov 12 18:33:11 CET 2010
Have plotted two samples as you suggested [ plot
(d$counts[,2],d$counts[,3],log="xy")] and saved the file on the FTP server.
Login using the username 'anonymous' and use your email address as password.
get /edupload/logplot.eps as well as get /edupload/plot2.eps and get
Which are plot asinh(count) graphs you suggested but must confess not
sure if plotted correctly, plot(d$counts[,2],asinh(d$counts[,2]))
but they are plots 1 and 2 respectively.
There does seem to be some correlation on the log-log plot.
On 19:59, Simon Anders wrote:
> On 11/11/2010 11:44 AM, A Gossner wrote:
>> While using edgeR to analysis my Tag-seq data, no matter which way I
>> analyse the data common or tagwise dispersion the FDR value is always 1.
>> Typical output is shown below;
>>  4.884378
> A common dispersion value of 4.8 means that your expresiion typically
> varies between replicates by 220% (that's sqrt(4.8.)). In other words,
> there is only noise and no signal in your data -- or you are doing
> something fundamentally wrong.
> Look at some scatter plots, plotting the count values of one sample
> against the count values of a replicate sample on a log-log scale (or
> better, plot asinh(count) ). Do they seem to correlate?
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