normexp background correction
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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia
> Date: Thu, 3 Nov 2005 03:59:35 -0600 > From: Edoardo Giacopuzzi <gedoardo at="" bluebottle.com=""> > Subject: [BioC] normexp background correction > To: bioconductor at stat.math.ethz.ch > > I'm using limma package to perform microarray data analysis. I've > tried different backgorund correction methods, expecially normexp and > edwards. I've read that normexp is considered the best by now, but I > can't found any detailed information about it (how it works on data > and so on). > Does anyone know where I can get this kind of information? > > Thanks! > Edoardo (University of Brescia) I'm the author of the normexp method, but I haven't yet published a detailed description. Sorry. Gordon
Microarray limma Microarray limma • 764 views
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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia
>Date: Mon, 7 Nov 2005 22:14:25 +1100 (EST) >Subject: [BioC] normexp background correction >From: "Gordon K Smyth" smyth at wehi.edu.au >To: "Edoardo Giacopuzzi" gedoard at bluebottle.com >Cc: bioconductor at stat.math.ethz.ch > > > Date: Thu, 3 Nov 2005 03:59:35 -0600 > > From: Edoardo Giacopuzzi gedoardo at bluebottle.com > > Subject: [BioC] normexp background correction > > To: bioconductor at stat.math.ethz.ch > > > > I'm using limma package to perform microarray data analysis. I've > > tried different backgorund correction methods, expecially normexp and > > edwards. I've read that normexp is considered the best by now, but I > > can't found any detailed information about it (how it works on data > > and so on). > > Does anyone know where I can get this kind of information? > > > > Thanks! > > Edoardo (University of Brescia) > >I'm the author of the normexp method, but I haven't yet published a >detailed description. Sorry. > >Gordon It may help that normexp was used in the following two publications. The method was actually invented for use in the first publication, and the second publication is probably the best reference at this time. Regards Gordon Peart, M. J., Smyth, G. K., van Laar, R. K., Richon, V. M., Holloway, A. J., Johnstone, R. W. (2005). Identification and functional significance of genes regulated by structurally diverse histone deacetylase inhibitors. Proceedings of the National Academy of Sciences of the United States of America.102, 3697-3702. Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397-420.
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