[BioC] OSX location of bioconductor functions

[Bobby Prill]

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


On Mar 9, 2007, at 8:44 AM, James W. MacDonald wrote:

> Bobby Prill wrote:
>> As an aside, I can't imagine why the column names in ANY function   
>> would be changed.  These column names are essentially the  
>> external  interface to the function.  It seems like a very bad  
>> design decision  to just one day change "M" to "logFC."
>
> What has been changed is the output of a function (which is _not_  
> the external interface to the function), and IIRC the change was  
> made to better reflect what the column contained.
>
> The version of limma that had the columns labeled M and A still  
> does exist, and a simple downgrade to R-2.3.1 and a biocLite() will  
> get you there.
>
> Anyway, I'm not sure I follow your logic. Are you saying that the  
> output of _all_ functions once written should be inviolate? So no  
> change, no matter how incremental is allowed? Personally, I  
> couldn't disagree more with this stance. You cannot improve things  
> if you are not allowed to make changes to both the API and the output.
>
>
> Best,
>
> Jim
>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
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