I'm sort of new to the world of bioinformatics and microarrays data analysis, and I've been having some trouble with limma's 'separate channel analysis of two-color data'. I've tried to implement the pipeline as suggested in the user's guide, but I got an error message saying dimmensions of the objects in the argument of
> corfit <- intraspotCorrelation(MA, design) Error in intraspotCorrelation(MA, design) : The number of rows of the design matrix should match the number of channel intensities, i.e., twice the number of arrays
I checked the structure of the input objects and they seem to be fine:
> nrow(design)  8 > M<- as.matrix(MA$M) > dim(M)  45018 8
Any thoughts on what could be going on here? Of note, the data went through normalization by
nomalizeBetweenArrays, and then
avereps before trying the correlation fit.
I hope you can help me. Thanks in advance!