Question: problems with snapCGH readPositionalInfo processCGH
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gravatar for Dick Beyer
10.1 years ago by
Dick Beyer1.4k
Dick Beyer1.4k wrote:
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
cgh snapcgh • 585 views
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