[BioC] F.test and esApply

[Stephen Henderson]

Thanks 
Your reply is about half way there the rest was a problem with the model
formula. It's: 

> fun<-function(x){lm(histo~x)$coef[1]}
> f<-esApply(D.big,1,fun)

in case anyone cares!

Stephen


-----Original Message-----
From: rossini at blindglobe.net [mailto:rossini at blindglobe.net] 
Sent: Monday, October 06, 2003 4:17 PM
To: Stephen Henderson
Subject: Re: [BioC] F.test and esApply

Stephen Henderson <s.henderson at ucl.ac.uk> writes:

> Perhaps I am misunderstanding the way esApply works-- but trying to use lm
> gives me 
>
>> fun<-function(x){ lm(cov1~1, x)}
>> f<-esApply(D.big,1,fun)
> Error in eval(expr, envir, enclos) : numeric envir arg not of length one
>
> Which is mysterious???

No, you are returning a huge structure, not of length 1.  

Perhaps something like:

fun<-function(x){ lm(cov1~1, data=x)$coef[1]}

(untested, use str() on the results of an lm fit to find the results
you are looking for --  I think you can get vectors back as well, but
not sure).

best,
-tony




>
> S
>
> -----Original Message-----
> From: rossini at blindglobe.net [mailto:rossini at blindglobe.net] 
> Sent: Monday, October 06, 2003 3:58 PM
> To: Stephen Henderson
> Subject: Re: [BioC] F.test and esApply
>
>
> ? lm will handle factors, I think?
>
> best,
> -tony
>
> Stephen Henderson <s.henderson at ucl.ac.uk> writes:
>
>> I maybe being a bit obtuse but I'm trying to work out how to get an F
>> statistic for each gene using esApply. I have factors in pData not
numeric
>> data suitable for lm 
>> e.g.
>>
>>
>>
>> fun<-function(x){ ....? }
>>
>> f.vector<-esApply(eset,1, fun)
>>
>>
>> I can't find what I need in any of the literature. Does anyone know the
>> command/ function I need?
>>
>> Thanks
>> Stephen
>>
>>
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>
> -- 
> rossini at u.washington.edu            http://www.analytics.washington.edu/ 
> Biomedical and Health Informatics   University of Washington
> Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
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-- 
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC  (M/W): 206-667-7025 FAX=206-667-4812 | use Email

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