R help - Mar 2008 - p-adjust using Benjamn and Hochberg

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?

thanks,
k
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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
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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

Keizer_71 <christophe.lo at gmail.com> wrote in
news:15944523.post at talk.nabble.com: 
> 
> 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?
Two that I can think of:

A) Change your posting style. Start including reproducible code. You 
are making the audience guess at what pt might be. At the very least 
you could have included the results of str(pt).

B) Change the argument to p.adjust so that it is the vector of p-values 
rather than what is (probably) the entire dataframe.

See:

gt<-"9997 201674_s_at  0.327547396
9998      221013_s_at  0.834211067
9999      221685_s_at  0.185099475
"
gene.p<-read.table(file=textConnection(gt),header=FALSE)
pa<-p.adjust(gene.p$V3,method="BH")
> pa
[1] 0.4913211 0.8342111 0.4913211

-- 
David Winsemius