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Dick Beyer
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1.4k
@dick-beyer-26
Last seen 10.2 years ago
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:
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,
Dick
**********************************************************************
*********
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
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer