 Hi everyone, 
 
As I read the "snapCGH: Segmentation, Normalization and Processing of aCGH Data User´s Guide" I became really excited with all the features in it to analyse CGH data and because it is designed to be used in conjunction with limma package, which I have already been using. I have done the practicals and browsed the main functions using the data given in the package.

After this stage I wanted to deal with a real data set so I downloaded a CGH experiment from GEO (Gene Expression Omnibus) and put it on R workspace using the GEOquery package. After that I converted the GEO DataSet into an MAList to be able to use the data with snapCGH package.

Despite of this, when I used the function processCGH it gave me an error:

 

> MA2 <- processCGH(MA, method.of.averaging=mean, ID="ID")

Error in processCGH(MA, method.of.averaging = mean, ID = "ID") : $design component is null

 

So, then I managed to to make the design column, but it gave me an error, but a different one:

 

> MA$design <- rep(1,10)

> MA2 <- processCGH(MA, method.of.averaging=mean, ID="ID")

Error in order(na.last, decreasing, ...) : argument 1 is not a vector

 

Therefore, if MA is an object of class MAList this function should work. I do not see what is wrong. Isn´t the snapCGH package compatible with the GEO datasets?

There is also another thing. In the examples folder of the package, the clones.info file has the columns Chromosome and Position, but in the dataset from GEO there is only the Entrez.GeneID identifier. Do you know of anyway I could convert one into another?


Best regards

João Fadista
Ph.d. student


 	
 	 Danish Institute of Agricultural Sciences	
Research Centre Foulum	
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