[BioC] Bioconductor documentation

[Gordon Smyth]

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