Dear all,
 
I am having some problems dealing with the function processCGH in the snapCGH package. My data is from a GEO dataset. I have converted this data into an MAList and added the columns "Chr" and "Position" to the MA$genes dataframe.
 
After this I used the function process CGH but it gave me an error:
 
> MA5 <- processCGH(MA4, method.of.averaging = mean, ID="ID")

Processing chromosome 1

Processing chromosome 10

Processing chromosome 11

Processing chromosome 12

Processing chromosome 13

Processing chromosome 14

Processing chromosome 15

Processing chromosome 16

Processing chromosome 17

Processing chromosome 18

Processing chromosome 19

Processing chromosome 2

Processing chromosome 20

Processing chromosome 21

Processing chromosome 22

Error in if (kb >= chrominfo$centromere[chr]) median(vec[clones.info$Chr == : 

missing value where TRUE/FALSE needed

 

Does anyone have any idea of what could be wrong? Thanks in advance...

Best regards

João Fadista
Ph.d. student


 	
 	 Danish Institute of Agricultural Sciences	
Research Centre Foulum	
Dept. of Genetics and Biotechnology	
Blichers Allé 20, P.O. BOX 50	
DK-8830 Tjele	
 	
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E-mail:	 Joao.Fadista@agrsci.dk <mailto:Joao.Fadista@agrsci.dk> 	
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