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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