DESeq2 results

RNA-Seq with Bioconductor in R

Mary Piper

Bioinformatics Consultant and Trainer

DESeq2 results table

mcols(wt_res)

DESeq2_results_columns

RNA-Seq with Bioconductor in R
head(wt_res, n=10)

log2 fold change (MAP): condition fibrosis vs normal 
Wald test p-value: condition fibrosis vs normal 
data frame with 6 rows and 6 columns
                           baseMean   log2FoldChange             lfcSE             stat
                          <numeric>        <numeric>         <numeric>        <numeric>
ENSMUSG00000102693                0               NA                NA               NA
ENSMUSG00000064842                0               NA                NA               NA
ENSMUSG00000051951 19.5084656230804 3.55089043143673 0.648400500074659 4.66871842838828
ENSMUSG00000102851                0               NA                NA               NA
ENSMUSG00000103377                0               NA                NA               NA
ENSMUSG00000104017                0               NA                NA               NA
                                 pvalue                 padj
                              <numeric>            <numeric>
ENSMUSG00000102693                   NA                   NA
ENSMUSG00000064842                   NA                   NA
ENSMUSG00000051951 3.03084428526558e-06 1.93776447202312e-05
ENSMUSG00000102851                   NA                   NA
ENSMUSG00000103377                   NA                   NA
ENSMUSG00000104017                   NA                   NA
RNA-Seq with Bioconductor in R

Significant DE genes - summary

summary(wt_res)

deseq2 summary

RNA-Seq with Bioconductor in R

Significant DE genes - fold-change threshold

wt_res <- results(dds_wt, 
                  contrast = c("condition", "fibrosis", "normal"), 
                  alpha = 0.05, 
                  lfcThreshold = 0.32)

wt_res <- lfcShrink(dds_wt, 
                    contrast=c("condition", "fibrosis", "normal"), 
                    res=wt_res)
RNA-Seq with Bioconductor in R

Significant DE genes - summary

summary(wt_res)

deseq2 summary lfc_threshold

RNA-Seq with Bioconductor in R

Results - annotate

library(annotables)

grcm38

annotables_grcm38

RNA-Seq with Bioconductor in R

Results - extract

wt_res_all <- data.frame(wt_res) %>% 
              rownames_to_column(var = "ensgene") %>%
              left_join(x = wt_res_all, 
                        y = grcm38[, c("ensgene", "symbol", "description")], 
                        by = "ensgene")                    
View(wt_res_all)

merged_all_results

RNA-Seq with Bioconductor in R

Significant DE genes - arrange

wt_res_sig <- subset(wt_res_all, padj < 0.05)

wt_res_sig  <- wt_res_sig %>%  
        arrange(padj)

View(wt_res_all)

merged_all_results

RNA-Seq with Bioconductor in R

sig genes

RNA-Seq with Bioconductor in R

Let's practice!

RNA-Seq with Bioconductor in R

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