[BioC] problems with snapCGH readPositionalInfo processCGH

Dick Beyer dbeyer at u.washington.edu
Wed Sep 9 19:50:53 CEST 2009

Hello to snapCGH users,

I'm trying to analyze Agilent CGH arrays and I'm using the snapCGH package.

I follow the user's guide just fine until I get to processCGH when I get the 

Error in order(MA$genes$Chr, MA$genes$Position) : 
  argument 2 is not a vector

The processCGH function is expecting to see a column named Position. (You can see this if you look at the line  
ord <- order(MA$genes$Chr, MA$genes$Position)
in the processCGH() function)

However, processing the Agilent input files with readPositionalInfo(), I get columns named Chr, Start, End.  Am I ok if I simply rename the Start column Position, and then run processCGH?

Here is a snip of the genes slot:

  Row Col ProbeUID ControlType      ProbeName                 GeneName            SystematicName Description Chr     Start       End
4   1   4        3           0 A_67_P03794163                    Glra2  chrX:160482222-160482281        null  23 160.48222 160.48228
5   1   5        5           0 A_67_P09430975 chrX:132217816-132217875  chrX:132217816-132217875        null  23 132.21782 132.21787
6   1   6        7           0 A_67_P07692235                    Ylpm1 chr12:085949415-085949474        null  12  85.94942  85.94947
7   1   7        9           0 A_67_P05354984                    Rab3b  chr4:108413892-108413951        null   4 108.41389 108.41395

This is my first CGH analysis, so if anyone thinks I'm headed off in the wrong 
direction, please let me know.  I'd be very grateful for any suggestions.

Thanks very much,
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
			Seattle, WA 98105-6099

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