[BioC] Bioconductor documentation

[Naomi Altman]

I hit return too soon.  I see what Gordon means.  I will have a look at how 
to write a weight function. --Naomi

At 09:28 AM 8/31/2004 +1000, Gordon Smyth wrote:
>At 11:33 PM 30/08/2004, Naomi Altman wrote:
>>The vignettes are great - perhaps I should not call them 
>>"tutorials".  But like other documentation of this type (the book "SAS 
>>for Mixed Models" comes to mind), it is hard to generalize from the 
>>examples.  We need both the vignettes and the internal documentation.  We 
>>need good but explicit defaults for the general user, and the option to 
>>change these defaults for the expert user.
>>
>>Here is an example where the documentation is OK, but the option to 
>>change the defaults is too limited.
>>
>>Both limma and marray allow the user read only a limited set of columns 
>>from gpr and spot files.  Why not have this as the default, and let the 
>>user decide if they want to read in other columns? Some of my clients 
>>like to filter spots based on quantities like the difference between the 
>>median and mean spot intensity, the sd of intensity, etc.  They currently 
>>need to flag spots before importing into Bioconductor because they cannot 
>>read these other columns readily into an marrayRaw object.
>
>The wt.fun argument to read.maimages() function in limma already provides 
>the capability to filter or weights spots based on any number of columns 
>in the original file. So there no need to read in the extra columns or to 
>flag spots before importing. The computation of the flags is done at the 
>time of import.
>
>The help document for read.maimages() says:
>      Spot quality weights may be extracted from the image analysis
>      files using a ready-made or a user-supplied weight function
>      'wt.fun'. 'wt.fun' may be any user-supplied function which accepts
>      a data.frame argument and returns a vector of non-negative
>      weights. The columns of the data.frame are as in the image
>      analysis output files. See 'QualityWeights' for provided weight
>      functions.
>
>I admit that this is brief, but it does seem explicit.
>
>I know that reading in extra columns can be convenient for other purposes. 
>The reason why I decided not to implement this in limma was explained in a 
>post to this list on 22 July:
>https://www.stat.math.ethz.ch/pipermail/bioconductor/2004-July/005434.html
>
>Gordon
>
>>--Naomi
>>
>>Naomi S. Altman                                814-865-3791 (voice)
>>Associate Professor
>>Bioinformatics Consulting Center
>>Dept. of Statistics                              814-863-7114 (fax)
>>Penn State University                         814-865-1348 (Statistics)
>>University Park, PA 16802-2111
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111