[BioC] discrepancies using different gcRMA

[Zhijin Wu]

The major change in the  new version is to stop  gene specific 
adjustment  for  the probes that appear to have only background level  
intensities. There is no option to generate the older version adjustment 
since that is considered not desirable.

Wen Huang wrote:
> Hi,
>
> I have a question about the difference between different versions of 
> gcRMA.
>
> I recently (a couple weeks ago) updated R and Bioconductor and tried 
> to reproduce some analysis I have done back in the summer. I found 
> that the expression values I got using simply the function "gcrma()" 
> were different. I checked the documentation and it says a few options 
> were added but not really helpful to my question.
>
> I just wonder if anybody knows a quick way to add some options to the 
> new version of gcRMA and reproduce what the old gcRMA did before.
>
> Thanks a lot,
> Wen
>
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-- 
-------------------------------------------
Zhijin (Jean) Wu
Assistant Professor of Biostatistics
Brown University, Box G-S121
Providence, RI  02912

Tel: 401 863 1230
Fax: 401 863 9182
http://www.stat.brown.edu/zwu