Wed, Jan 14, 2015
Wed, Jan 14, 2015 at 8:37 PM
Customer: I have run gene expression microarrays (Affymetrix), and my experimental design requires a two way ANOVA statistical approach, which Affy's Transcriptome Analysis Console does not appear to offer. In addition, I need to normalize my data to a small set of genes (above and beyond the typical Affy gene list) of 5-6 genes. I have not been able to get answers to these two major issues by working with representatives with Affy (the turnaround time of conversations is extremely slow). I have the ARR, CEL, image files, and CHP files from Affy's software (Expression Console)...
Thu, Jan 15, 2015 at 8:43 AM
AccuraScience LB: Indeed, Besides the programs Affy offers, a number of tools are available with the Bioconductor project (http://www.bioconductor.org/) which allows normalization, expression quantification and differential expression analysis to be conducted in more meaningful manners. For instance, dchip methods allows normalization to be performed on an invariant subset of genes (whose rank orders do not change across chips), RMA method allows "quantile normalization" following probe-level log transform of the original data. Both methods work considerably better than Affy's scaling-based normalization method. If you prefer to do scaling-based normalization with 5-6 selected genes, we could write customized scripts to accomplish this goal. Two-way ANOVA can also be done in R - on which Bioconductor is based. The CEL files and (possibly) CHP files are all what would be required for us to do this work.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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