CSF Bulk 2. Differential Expression CSF vs PBMC

About the Data

DESeq2 analysis of CSF and PBMC myeloid and lymphoid cells with design = ~ 0 + group the groups include: PBMC_Myel, PBMC_Lym, CSF_Myel, CSF_Lym. Differential expression between CSF and PBMC in either myeloid cells or lymphoid cells. n = 6 CSF samples and 6 PBMC samples each bulk sorted for myeloid and lymphoid cells.

library(DESeq2)
library(ggplot2)
library(cowplot)
library(pheatmap)
library(ggrepel)
library(grid)
library(rstatix)

Load Data

load("data/filt_dds_env.rda")
resultsNames(dds)

DEG Results

# difference between CSF vs PBMC in lymphoid cells
summary(results(dds, contrast=c("group", "CSF_Lym", "PBMC_Lym"), alpha=0.05))


# difference between CSF vs PBMC in myeloid cells
summary(results(dds, contrast=c("group", "CSF_Myel", "PBMC_Myel"), alpha=0.05))


# difference between Mye vs Lym in PBMC cells
summary(results(dds, contrast=c("group", "PBMC_Lym", "PBMC_Myel"), alpha=0.05))


# difference between Mye vs Lym in CSF cells
summary(results(dds, contrast=c("group", "CSF_Lym", "CSF_Myel"), alpha=0.05))

CSFvPBMCinLym <- results(dds, contrast=c("group", "CSF_Lym", "PBMC_Lym"), alpha=0.05)
CSFvPBMCinLym$gene <- rowData(dds)$gene_name

CSFvPBMCinMye <- results(dds, contrast=c("group", "CSF_Myel", "PBMC_Myel"), alpha=0.05)
CSFvPBMCinMye$gene <- rowData(dds)$gene_name

MYEvLYMinPBMC <- results(dds, contrast=c("group", "PBMC_Myel", "PBMC_Lym"), alpha=0.05)
MYEvLYMinPBMC$gene <- rowData(dds)$gene_name

MYEvLYMinCSF <- results(dds, contrast=c("group", "CSF_Myel", "CSF_Lym"), alpha=0.05)
MYEvLYMinCSF$gene <- rowData(dds)$gene_name

write.csv(CSFvPBMCinLym, "writes/CSFvPBMCinLym.csv")
write.csv(CSFvPBMCinMye, "writes/CSFvPBMCinMye.csv")

plotMA(CSFvPBMCinLym, ylim=c(-10,10), main = "CSF v PBMC in LYM")
plotMA(CSFvPBMCinMye, ylim=c(-10,10), main = "CSF v PBMC in MYE")

Volcano plots of DEGs

library(EnhancedVolcano)

EnhancedVolcano(CSFvPBMCinMye,
    lab = CSFvPBMCinMye$gene,
    x = 'log2FoldChange',
    y = 'padj',
    title = 'CSFvPBMCinMye',
    pCutoff = 10e-3,
    FCcutoff = 2,
    pointSize = 2.5, ylim=c(0,115),
    labSize = 4.0,
    col=c('grey', 'grey', 'grey', 'grey30'),
    colAlpha = 1)
ggsave(filename = "plots/1.PUB/CSVvPBMCinMye.svg", width = 4.5, height = 6)

EnhancedVolcano(CSFvPBMCinLym,
    lab = CSFvPBMCinLym$gene,
    x = 'log2FoldChange',
    y = 'padj',
    title = 'CSFvPBMCinLym',
    pCutoff = 10e-3,
    FCcutoff = 2,
    pointSize = 2.5, ylim=c(0, 50),
    labSize = 4.0,
    col=c('grey', 'grey', 'grey', 'grey30'),
    colAlpha = 1)
ggsave(filename = "plots/1.PUB/CSVvPBMCinLym.svg", width = 4.5, height = 6)

sessionInfo()