Load DESeq2:
rr if (!requireNamespace(, quietly = TRUE)) install.packages() BiocManager::install(2, version = .8) library(DESeq2)
Load the Data table. I want to just start with the KRY85 auxin and the N2 auxin b/c I think this is the main comparison that actually shows differential expression.
rr sample_table_aux85_auxN2 <- read.table(../sample_table_N2_KRY_Auxin.txt, header = TRUE, sep = ‘’) HTseq_85aux_N2aux <- DESeqDataSetFromHTSeqCount(sampleTable = sample_table_aux85_auxN2, directory = ‘../HTSeq_85aux_N2aux’,design = ~ Condition)
OK start with looking at the data
rr HTseq_85aux_N2aux_vsd <- vst(HTseq_85aux_N2aux, blind = FALSE) plotPCA(HTseq_85aux_N2aux_vsd, intgroup=c(, )) glMDSPlot(HTseq_85aux_N2aux_vsd, groups=Condition)
rr HTseq_85aux_N2aux_DEseq2 <- DESeq(HTseq_85aux_N2aux) HTseq_85aux_N2aux_results <- results(HTseq_85aux_N2aux_DEseq2, contrast = c(, 85_aux, 2_aux)) HTseq_85aux_N2aux_results summary(HTseq_85aux_N2aux_results)
rr install.packages() library() select <- order(rowMeans(counts(HTseq_85aux_N2aux_DEseq2, normalized = TRUE)), decreasing =TRUE)[1:20] ntd <- normTransform(HTseq_85aux_N2aux) df <- as.data.frame(colData(HTseq_85aux_N2aux_DEseq2)[,c(, )]) pheatmap(assay(ntd, select)) glScatter(df)
rr if (!requireNamespace(, quietly = TRUE)) install.packages() BiocManager::install(, version = .8) library(Glimma)
library(DESeq2) library(edgeR) BiocManager::install(, version = .8) library(DEFormats) dge = as.DGEList(HTseq_85aux_N2aux_DEseq2) glMDSPlot(dge, path = tmp) browseURL(file.path(tmp,,-Plot.html)) status <- as.numeric(HTseq_85aux_N2aux_results\(padj < .1) annotations <- data.frame(GeneID = rownames(HTseq_85aux_N2aux_results), symbol = HTseq_85aux_N2aux_results\)symbol)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomeInfoDb", version = "3.8")Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1
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BiocManager::install("Glimma", version = "3.8")Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'Glimma'
also installing the dependencies ‘limma’, ‘edgeR’
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/var/folders/gn/l93zgf014_5_5fq9lwsrr9psypd4gx/T//Rtmp89YoQH/downloaded_packageslibrary(Glimma)package ‘Glimma’ was built under R version 3.5.2status <- as.numeric(HTseq_85aux_N2aux_results$padj < .1)
anno_gene <- data.frame(GeneID=rownames(HTseq_85aux_N2aux_results), symbol = rownames(HTseq_85aux_N2aux_results))
glMDPlot(HTseq_85aux_N2aux_results, status = status, counts = counts(HTseq_85aux_N2aux_DEseq2, normalized = TRUE), groups = HTseq_85aux_N2aux_DEseq2$Condition, transform = TRUE, samples = colnames(HTseq_85aux_N2aux_DEseq2), anno = anno_gene, path = './', folder = "glimma_MD", launch = FALSE)