[BioC] Interaction term logFC
Neetha [guest]
guest at bioconductor.org
Wed Jul 16 19:10:40 CEST 2014
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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