Thank you very much. I'll keep that in my mind. With Respects, Kaj 2557-07-29 22:06 GMT+07:00, Sean Davis <sdavis2 at="" mail.nih.gov="">: > Hi, Kaj. > > There is no general answer to your question, I do not think. However, > assuming that a statistical test was applied in both cases, one would need > to evaluate the statistical evidence to make an informed decision. I will > say that while machine learning approaches often include feature selection, > the most common way to get a set of genes that differentiates two > phenotypes or groups of samples is using differential gene expression > hypothesis testing. > > Sean > > > > On Tue, Jul 29, 2014 at 11:00 AM, Kaj Chokeshaiusaha [guest] < > guest at bioconductor.org> wrote: > >> Dear R helpers, >> >> I'm confused about the applications of ranked top genes generated from >> multiple learning datasets normally used for supervised classification >> and >> those directly acquired from differential gene expression test from >> original data. >> >> With the same cut-off (like FDR<0.05) and nice classification result, are >> the ranked gene list better candidate for further biological validation >> (PCR) and gene enrichment analysis? >> >> With Respects, >> Kaj >> >> -- output of sessionInfo(): >> >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] plsgenomics_1.2-6 MASS_7.3-33 limma_3.20.8 >> [4] RankProd_2.36.0 CMA_1.22.0 Biobase_2.24.0 >> [7] BiocGenerics_0.10.0 e1071_1.6-3 >> >> loaded via a namespace (and not attached): >> [1] class_7.3-10 tools_3.1.0 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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 >> >