thanks Mike, this was very helpful!


On Fri, Apr 5, 2013 at 12:58 PM, Michael Love
<michaelisaiahlove@gmail.com>wrote:

> hi Bas,
>
> This is a direct consequence of the method of Benjamini and Hochberg. The
> paper is quite accessible and worth a look:
> http://www.jstor.org/stable/2346101
>
> See formula (1) under "False Discovery Rate Controlling Procedure".
>
> All the p-values p_i up to p_k also get rejected at the FDR q.
>
> for a visualization of this formula, take a few sorted p-values with
> adjusted p-value written above:
>
> p <- sort(c(.01,.2,.21,.22,.5,.51,.52,.8,.9))
> padj <- p.adjust(p, method="BH")
> plot(p,ylim=c(0,1),xlim=c(0,length(p)))
> text(seq_along(p),p,round(padj,3),pos=3)
> abline(0,padj[4]/length(p))
>
> here, k = 4, m=length(p), and q = padj[4].
>
>
> Mike
>
>
>
> On Fri, Apr 5, 2013 at 10:16 AM, Bas ter Braak <basterbraak@gmail.com>wrote:
>
>> Hi Steve,
>>
>> Thanks for your reply. No, the adjusted p-values are not equal to 1.
>> Although the regular p-values vary from 0.0000225 to 0.000769, the
>> adjusted
>> p-values are exactly 0.069652712348149. And this for 147 DEGs. Is there
>> something wrong with my code in R?
>> thanks,
>>
>> Bas
>> On Thu, Apr 4, 2013 at 4:13 PM, Steve Lianoglou <
>> mailinglist.honeypot@gmail.com> wrote:
>>
>> > Hi,
>> >
>> >
>> > On Thursday, April 4, 2013, Bas ter Braak [guest] wrote:
>> >
>> >>
>> >> Dear list,
>> >>
>> >> I was converting the p values of my DEG list to adjusted p-values
>> (using
>> >> benjamin Hochberg) and found out that many adjusted p-values have the
>> exact
>> >> same value. (using topTable from limma package)
>> >> Is this normal and what is the reason for this observation?
>> >
>> >
>> > Are the identical values that you observe equal to 1 by any chance?
>> >
>> >
>> >
>> > --
>> > Steve Lianoglou
>> > Defender of The Thesis
>> >  | Memorial Sloan-Kettering Cancer Center
>> >  | Weill Medical College of Cornell University
>> > Contact Info: http://cbio.mskcc.org/~lianos/contact
>> >
>>
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>>
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>
>

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