[R] p-adjust using Benjamn and Hochberg

[Charles C. Berry]

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
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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