[BioC] DESeqs two-factor two-level, interaction is interested

Shawn [guest] guest at bioconductor.org
Sat May 17 08:00:51 CEST 2014


Hello Mike,

Please allow me ask a basic question.  What does 'log2FoldChange' in the results of  DESeq2 analysis really mean for the interaction of a two-factor two-level design?  Is it possible to compare 'Factor A level 1' to ' Factor A level 2' or other similar comparison? 

Here are the part of codes I used:


dds <- phyloseq_to_deseq2(phyloseq.obj, design=~ Treatment*Day)

colData(dds)$Treatment<- factor(colData(dds)$Treatment,levels=c("Control","Treat"));
colData(dds)$Day<- factor(colData(dds)$Day,levels=c("A","B"))

dds$Treatment<- relevel(dds$Treatment, "Control")
dds$Day<- relevel(dds$Day, "A")

dds <- DESeq(dds, fitType="local",betaPrior=FALSE)

Shawn


 -- output of sessionInfo(): 

sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
 [1] parallel  grid      splines   stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ecodist_1.2.9           Biostrings_2.32.0       doParallel_1.0.8        foreach_1.4.2          
 [5] iterators_1.0.7         metagenomeSeq_1.6.0     gplots_2.13.0           limma_3.20.1           
 [9] Biobase_2.24.0          DESeq2_1.4.5            GenomicRanges_1.16.3    GenomeInfoDb_1.0.2     
[13] RcppArmadillo_0.4.300.0 Rcpp_0.11.1             XVector_0.4.0           IRanges_1.22.6         
[17] BiocGenerics_0.10.0     locfit_1.5-9.1          phangorn_1.99-7         genefilter_1.46.1      
[21] adephylo_1.1-6          scatterplot3d_0.3-35    analogue_0.12-0         rgl_0.93.996           
[25] princurve_1.1-12        labdsv_1.6-1            mgcv_1.7-29             indicspecies_1.7.1     
[29] biom_0.3.13             ggplot2_0.9.3.1         plyr_1.8.1              phyloseq_1.9.2         
[33] pamr_1.54.1             cluster_1.15.2          survival_2.37-7         vegan_2.0-10           
[37] lattice_0.20-29         permute_0.8-3           RColorBrewer_1.0-5      matrixStats_0.8.14     
[41] MASS_7.3-33             ape_3.1-1               ade4_1.6-2              nlme_3.1-117           

loaded via a namespace (and not attached):
 [1] adegenet_1.4-1       annotate_1.42.0      AnnotationDbi_1.26.0 bitops_1.0-6        
 [5] brglm_0.5-9          caTools_1.17         codetools_0.2-8      colorspace_1.2-4    
 [9] data.table_1.9.2     DBI_0.2-7            digest_0.6.4         fastmatch_1.0-4     
[13] gdata_2.13.3         geneplotter_1.42.0   gtable_0.1.2         gtools_3.4.0        
[17] httpuv_1.3.0         igraph_0.7.0         KernSmooth_2.23-12   Matrix_1.1-3        
[21] multtest_2.20.0      munsell_0.4.2        phylobase_0.6.8      proto_0.3-10        
[25] R.methodsS3_1.6.1    reshape2_1.4         RJSONIO_1.2-0.2      RSQLite_0.11.4      
[29] scales_0.2.4         shiny_0.9.1          stats4_3.1.0         stringr_0.6.2       
[33] tools_3.1.0          XML_3.98-1.1         xtable_1.7-3         zlibbioc_1.10.0     


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