Simon - just read your message on negative illumina data. I'm faced with the same thing and it is definitely fluorescent intensities with negative values. It ranges from approx. -200 to +20,000. I'm thinking that it's maybe background subtracted and that's where the negative values are coming from. If that's the case could we add a constant to all the data (equal to ~200) to bring it up to minimum of 0.0 or thereabouts? Matt ---------------------- Matthew Arno, Ph.D. Genomics Centre Manager King's College London ? Office 3.129 Franklin-Wilkins Building 150 Stamford Street London SE1 9NH UK telephone (office): +44 (0)20 7848 4286 telephone (lab): +44 (0)20 7848 4263 website: www.kcl.ac.uk/genomics email: matthew.arno at kcl.ac.uk ? ? The contents of this email are strictly confidential. It may not be transmitted in part or in whole to any other individual or groups of individuals. This email is intended solely for the use of the individual(s) to whom they are addressed and should not be released to any third party without the consent of the sender.

Hi Matt you could try the function 'vsn2' (package: vsn), it is designed to find that type of additive offset automatically (the mathematical details are a bit more complex but that's the gist of it). Let me know if the vignette or the accompanying paper are unclear. Best wishes Wolfgang Il Jun/8/11 6:44 PM, Arno, Matthew ha scritto: > Simon - just read your message on negative illumina data. I'm faced with the same thing and it is definitely fluorescent intensities with negative values. It ranges from approx. -200 to +20,000. I'm thinking that it's maybe background subtracted and that's where the negative values are coming from. If that's the case could we add a constant to all the data (equal to ~200) to bring it up to minimum of 0.0 or thereabouts? > > Matt > > ---------------------- > Matthew Arno, Ph.D. > Genomics Centre Manager > King's College London > > Office 3.129 > Franklin-Wilkins Building > 150 Stamford Street > London > SE1 9NH > UK > telephone (office): +44 (0)20 7848 4286 > telephone (lab): +44 (0)20 7848 4263 > > website: www.kcl.ac.uk/genomics > > email: matthew.arno at kcl.ac.uk > > > The contents of this email are strictly confidential. It may not be transmitted in part or in whole to any other individual or groups of individuals. > This email is intended solely for the use of the individual(s) to whom they are addressed and should not be released to any third party without the consent of the sender. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber