[BioC] Interaction term logFC

[Neetha [guest]]

Hi,


I am using DESeq2 for my RNAseq data analysis. My design has two strains and two conditions. I did my analysis with DESeq2 v 1.4.5 with the design
dds1 <- DESeqDataSetFromMatrix(countData=counts, colData=design, design=~ Colony + Treatment + Colony:Treatment)
dds1 <- DESeq(dds1, test="LRT", reduced=Colony + Treatment)
>resultsNames (dds1)
[1] "Intercept"  "Colony_1_vs_2" "Treatment_1_vs_2"    "Colony1.Treatment1"

"Colony1.Treatment1" is the interaction term. Am I right? I don't understand what the log2fold change represents. I read the vignette (last updated May 2014) as well several discussions online, but I am not sure I understand the concept. For those genes with FDR corrected p values below 0.05, when go back and check the VST counts/raw reads I see trends. Could you please help me understand what the log2foldchange means?
Thanks in advance.
Neetha


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] DESeq2_1.4.5            RcppArmadillo_0.4.320.0 Rcpp_0.11.2            
[4] GenomicRanges_1.16.3    GenomeInfoDb_1.0.2      IRanges_1.22.9         
[7] BiocGenerics_0.10.0     BiocInstaller_1.14.2   

loaded via a namespace (and not attached):
 [1] annotate_1.42.0      AnnotationDbi_1.26.0 Biobase_2.24.0       DBI_0.2-7           
 [5] genefilter_1.46.1    geneplotter_1.42.0   grid_3.1.1           lattice_0.20-29     
 [9] locfit_1.5-9.1       RColorBrewer_1.0-5   RSQLite_0.11.4       splines_3.1.1       
[13] stats4_3.1.1         survival_2.37-7      tools_3.1.1          XML_3.98-1.1        
[17] xtable_1.7-3         XVector_0.4.0       


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