Question: DESeq analysis of resistance data
4.8 years ago by
Guest User • 12k
Guest User • 12k wrote:
Hello, I am analysing RNASeq data from cancer cell lines. I have 3 groups with n=5 in each group. One group is sensitive to a drug, the second group has been selected for clones which have become resistant to the drug. The third group is a control, vehicle-treated group. I have used DESeq2 before to compare two groups but I'd be interested in advice on how to analyse these data please. I am interested in identifying differential changes in the resistant group which might be leading to the acquired resistance. Would analysing these data using an ANOVA model be appropriate? Thanks, Dave -- output of sessionInfo(): R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  DESeq2_1.4.5 RcppArmadillo_0.4.300.0 Rcpp_0.11.1  GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 IRanges_1.22.7  BiocGenerics_0.10.0 loaded via a namespace (and not attached):  annotate_1.42.0 AnnotationDbi_1.26.0 Biobase_2.24.0  DBI_0.2-7 genefilter_1.46.1 geneplotter_1.42.0  grid_3.1.0 lattice_0.20-29 locfit_1.5-9.1  RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.1.0  stats4_3.1.0 survival_2.37-7 XML_3.98-1.1  xtable_1.7-3 XVector_0.4.0 -- Sent via the guest posting facility at bioconductor.org.
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