[BioC] OSX location of bioconductor functions

[Bobby Prill]

Gordon and Jim,

Thanks for the education on Bioconductor and Limma.  I'm very  
grateful that this software is actively developed, and works.  I can  
see that most of my frustration stems from not knowing how to  
efficiently pull results out of the various R objects.

- Bobby


On Mar 10, 2007, at 4:24 PM, James W. MacDonald wrote:

> Gordon Smyth wrote:
>> Wish I'd read this exchange before making my own long-winded  
>> reply  :)
>>
>> BTW, fit$Amean is always just a vector so the test ncol(fit$Ameans)
>> shouldn't be necessary.
>
> I cribbed that out of topTable() (I believe). I didn't think Ameans
> would ever be a matrix, but defensive programming and all that...
>
> Best,
>
> Jim
>
>
>>
>> Cheers
>> Gordon
>>
>>> [BioC] OSX location of bioconductor functions
>>> James W. MacDonald jmacdon at med.umich.edu
>>> Fri Mar 9 18:58:02 CET 2007
>>>
>>> Hi Bobby,
>>>
>>> Yes there is a much better way to get what you want. Note that the
>>> MArrayLM object returned by eBayes() is just a list. The M values  
>>> are
>>> held in the 'coefficients' list member (or whatever the technical  
>>> term
>>> is), and the A values are in the 'Ameans' list member.
>>>
>>> So to get what you want, you would do this:
>>>
>>> M <- fit$coefficients[,1] ## we get coef = 1
>>> A <- if(ncol(fit$Ameans) > 1) rowMeans(fit$Ameans) else fit$Ameans
>>>
>>> Best,
>>>
>>> Jim
>>>
>>> Bobby Prill wrote:
>>>> Jim,
>>>>
>>>> I understand what you're saying.  My problem is more with the "R
>>> way  of
>>>> doing things," which takes some getting used to.
>>>>
>>>> Perhaps you can recommend a better way for me to do the  
>>>> following:  I
>>>> want the M and A values for every probe on a chip.  This is what  
>>>> I  do,
>>>> which has always looked ugly to me:
>>>>
>>>> ## the number of probes
>>>> N = dim(exprs(eset))[1]
>>>>
>>>> ## ask topTable to return for every probe
>>>> T = topTable(fit, coef=1, adjust="fdr", n=N)
>>>>
>>>> ## put back in original probe order
>>>> ord = order(as.integer(rownames(T)))
>>>> T = T[ord,]
>>>>
>>>> T$A
>>>> T$M
>>>>
>>>> There must be a better way?
>>>>
>>>> - Bobby
>>
>>
>
>
> -- 
> James W. MacDonald
> University of Michigan
> Affymetrix and cDNA Microarray Core
> 1500 E Medical Center Drive
> Ann Arbor MI 48109
> 734-647-5623
>
>
>
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