Re: [R] p-adjust using Benjamn and Hochberg

From: Charles C. Berry <cberry_at_tajo.ucsd.edu>
Date: Sun, 09 Mar 2008 12:05:29 -0700

On Sun, 9 Mar 2008, Keizer_71 wrote:

>
> Hello,
>
> I am trying to use the p.adjust function for multiple testing.
>
> here is what i have
>
> 9997 201674_s_at 0.327547396
> 9998 221013_s_at 0.834211067
> 9999 221685_s_at 0.185099475
>
> I import them from excel have have the gene symbol as well as the pvalue
>
> here is the issue
>
>> pa<-p.adjust(pt,method="BH")

> Error in p[nna] : object is not subsettable
> In addition: Warning message:

> In is.na(p) : is.na() applied to non-(list or vector) of type 'closure'
>> adjust<-sum(pa<0.1)
>
> Is there anything i need to change?

Your understanding of what pt is, perhaps?

Try

         str( pt )

to learn more.

If it turns out that pt is not a vector of p-values (and the error message suggests that it might be stats:::pt), then you have to figure out how to obtain a vector of p-values "from excel". The 'R Data Import/Export' Manual and 'An Introduction to R' are your friends.

HTH, Chuck

>
> thanks,
> k
> --
> View this message in context: http://www.nabble.com/p-adjust-using-Benjamn-and-Hochberg-tp15944523p15944523.html
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>
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Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry_at_tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901

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