[BioC] rowQ error

[Dennis.Burian at faa.gov]

Sorry, my intent was to return it to the list.

Needing devel explains why a cutoff of 0.5 only returned 674 probe sets
with nsFilter.  That had me scratching my head plenty but after the brain
fade with rowQ, I wasn't going to ask any questions until I was more sure
of my footing with the genefilter package.

Dennis Burian, Ph.D.
Functional Genomics Group
Civil Aerospace Medical Institute, AAM-610
6500 S. MacArthur Blvd.
Oklahoma City OK  73169
405-954-6087
dennis.burian at faa.gov


                                                                           
             Robert Gentleman                                              
             <rgentlem at fhcrc.o                                             
             rg>                                                        To 
                                       Dennis M Burian/AMC/FAA at FAA         
             01/31/2008 05:23                                           cc 
             PM                                                            
                                                                   Subject 
                                       Re: [BioC] rowQ error               
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           




Yes, then the right thing is to try out nsFilter, and if it works (or
doesn't), if you could return the thread to the mailing list, then all
will see its successful conclusion, (oh and you need to use the devel
version as nsFilter is broken in release).

  otherwise something like

   lowQ = rowQ(myexprset, floor(0.25*numberofsamples))
   upQ = rowQ(myexprset, ceiling(0.75*numberofsamples))
   iqr = upQ-lowQ
   good = iqr > median(iqr)
   newEset = myexprset[good,]



  thanks
    Robert


Dennis.Burian at faa.gov wrote:
> First, thanks for the quick reply and I'll look at nsFilter.  Per our
> discussion at the Introductory R course last November, the intent here is
> to keep the top 50% of genes based on IQR for differential expression
> testing.  I'm following the script in the Machine Learning module from
the
> course but I'm open to suggestion.
>
>
> Dennis Burian, Ph.D.
> Functional Genomics Group
> Civil Aerospace Medical Institute, AAM-610
> 6500 S. MacArthur Blvd.
> Oklahoma City OK  73169
> 405-954-6087
> dennis.burian at faa.gov
>

--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org