Question: Filtering by variance, IQR, etc.
12.6 years ago by
Mark W Kimpel • 830
Mark W Kimpel • 830 wrote:
I have been using what I consider to be non-biased filtering of low-variance genes using the method described in "Bioinformatics and Computational Biology Solutions using R and Bioconductor", R. Gentleman, et al., page 233 for some time and have recently run into some resistance from a colleague who claims that this type of filtering distorts FDR calculations because it introduces bias. His reasoning is that, since this method tends to filter out genes with higher p values and/or lower fold changes, that it is sort of a sneaky way of accomplishing just that. Of course, filtering by phenotype does introduce bias, but in this case I believe that by filtering based on the a priori assumption that we just aren't that interested in low variance genes for biologic reasons (even if statistically significant they will have very low fold changes and thus be of questionable meaning) that we aren't violating the statistical underpinnings of the analysis. I need some help in justifying this filtering step. Does anyone know of a peer-reviewed reference that gives a theoretical justification for its use of of any empiric experiments that show that it is legit? Thanks, Mark -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine
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