Hi,
    I've been using the limma normalizeBetweenArrays function to perform cyclic loess normalisation on single channel microarray data (non-log transformed signal intensities). Amongst the normalised signal intensities returned is one negative value. There is nothing 'odd' about the corresponding original value in the input signal intensity file. I presume that normalizeBetweenArrays is not expected to return negative signal intensities, and so any advice/insights would be gratefully received. I have already referred to the limma user guide, and to the 'normalizeBetweenArrays function help document' accessible online via R.

Many thanks.

Mike




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