R help - Feb 2011 - Pulling p values

Hi folks,

I'm doing ANOVA with multiple comparisons.  I've used both the TukeyHSD 
function and the multcomp procedure.  In both cases, I get some tantalizing
results such as this...

e = aov(lm(d.all[,(n+4)] ~ d.all[,4])

TukeyHSD(e)

  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = lm(d.all[, (n + 4)] ~ d.all[, 4], contrast = C))

$`d.all[, 4]`
                                 diff               lwr               upr       
p adj
10 mpk-0 mpk                                -0.677375 -1.1779417 -0.1768083  
0.0071092
30 mpk-0 mpk                               -1.074500 -1.5750667 -0.5739333   
0.0000656
30 mpk-10 mpk                             -0.397125 -0.8976917  0.1034417   
0.1369760

I ask for the pvalues and get...

i = h$pvalues
i
   10 mpk - 0 mpk              30 mpk - 0 mpk                 30 mpk - 10 mpk
   2.630022e-03                   2.288575e-05                      
5.863517e-02

It looks like a matrix, but it is a vector of length 3 and the third element,
for example, is....
> length(i)
[1] 3
> q = i[3]
> q
30 mpk - 10 mpk
     0.05863517

The contrast label is bound to the p-value as a single element.

Does anyone know how to extract just the p-value from this procedure?  Or a
simple way to generate these comparisons?

Thanks,

Bob Gallavan
An obvious newbie


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On 2011-02-26 04:12, Gallavan, Robert wrote:
> Hi folks,
>
> I'm doing ANOVA with multiple comparisons.  I've used both the
TukeyHSD  function and the multcomp procedure.  In both cases, I get some
tantalizing results such as this...
>
> e = aov(lm(d.all[,(n+4)] ~ d.all[,4])
>
> TukeyHSD(e)
>
>    Tukey multiple comparisons of means
>      95% family-wise confidence level
>
> Fit: aov(formula = lm(d.all[, (n + 4)] ~ d.all[, 4], contrast = C))
>
> $`d.all[, 4]`
>                                   diff               lwr               upr 
p adj
> 10 mpk-0 mpk                                -0.677375 -1.1779417 -0.1768083
0.0071092
> 30 mpk-0 mpk                               -1.074500 -1.5750667 -0.5739333 
0.0000656
> 30 mpk-10 mpk                             -0.397125 -0.8976917  0.1034417  
0.1369760
>
> I ask for the pvalues and get...
>
> i = h$pvalues
> i
>     10 mpk - 0 mpk              30 mpk - 0 mpk                 30 mpk - 10
mpk
>     2.630022e-03                   2.288575e-05                      
5.863517e-02
>
> It looks like a matrix, but it is a vector of length 3 and the third
element, for example, is....
>
>> length(i)
> [1] 3
>> q = i[3]
>> q
> 30 mpk - 10 mpk
>       0.05863517
>
> The contrast label is bound to the p-value as a single element.
Well, 'bound to' just means that you have a vector with names.
So you can just unname() it.

But do let us in on your secret: what's 'h'?
>
> Does anyone know how to extract just the p-value from this procedure?  Or a
simple way to generate these comparisons?
>
> Thanks,
>
> Bob Gallavan
> An obvious newbie
Newbies need to peruse the posting guide;
In particular, note the comment about HTML mail.

Peter Ehlers
>
>
> ------------------------------"This message is the property of
i3Global and may include confidential and/or proprietary information, and may be
used only by the person or entity to which it is addressed. If the reader of
this e-mail is not the intended recipient or his or her authorized agent, the
reader is hereby notified that any dissemination, distribution or copying of
this e-mail is prohibited. If you have received this e-mail in error, please
notify the sender by replying to this message and delete this e-mail
immediately."=============================>
> 	[[alternative HTML version deleted]]
>
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