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 The Animal Health Trust fights disease and injury in animals. Find out more about our work at http://www.aht.org.uk. This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the Animal Health Trust. If you are not the intended recipient of this email and its attachments, you must take no action based upon them, nor must you copy or show them to anyone without prior consent. Please contact the sender if you believe you received this email in error. This message has been sent from the Animal Health Trust. Registered address: Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU Registered charity no: 209642 [[alternative HTML version deleted]]

Dear Mike, Loess normalization (cyclic or otherwise) should only be applied after log transforming the intensities. normalizeBetweenArrays() will accept an EListRaw object containing unlogged intensities, but it will take logs before doing cyclic loess normalization. If you pass a numeric matrix to normalizeBetweenArrays(), then you are expected to have logged yourself. Best wishes Gordon > Date: Fri, 10 Jan 2014 17:10:25 +0000 > From: MIKE STARKEY <michael.starkey at="" aht.org.uk=""> > To: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: [BioC] limma - normalizeBetweenArrays function > > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}