[BioC] Post-justRMA "quality control"

[Claire Wilson]

> > boxplot(normalized.data,col=c(2,2,3,3))
> Error in boxplot.default(normalized.data, col = c(2, 2, 3, 3)) : 
>         invalid first argument
> >
> 
> > hist(normalized.data[1:2])
> Error in hist.default(normalized.data[1:2]) : 
>         `x' must be numeric
> >
> 
> If Ihave created an incompatible objecct with justRMA, how do I create
> the correct object type?  If not, what suggestions do you have.


I think the problem may be that you are passing the whole expression set, rather than just the expression levels themselves...try

hist(normalized.data at exprs[,1:2]) # should give you the first two samples
hist(normalized.data at exprs) # should give you a histogram of all expression levels

similarly for the boxplot, however if you change the matrix to a data frame, it will plot each chip seperately
boxplot(as.data.frame(normalized.data at exprs),col=c(2,2,3,3))

I am not sure the RNA degradation plot will work on normalised values

hope this helps

claire
 
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