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Analysis_Rat_PTSD_02_compareOutputs.R
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### Open .chp files from TAC
setwd('C:/Users/steph/Documents/R/UMB/PTSD_Rat_Project')
### Compare results from RMA normalization with subsequent testing
# Load R Stats
load('rda/mergedStats_RMA_R.rda',verbose=T)
# Load TAC STats
load('TAC/RMA_SingleRegion/MergedStats.rda',verbose=T) # res_stats
res_stats_P = sapply(res_stats, function(x) x[match(rownames(mergedStats) , x[,'ID']),'P-val'])
rownames(res_stats_P) = rownames(mergedStats)
colnames(res_stats_P) <- paste0(colnames(res_stats_P), "_P")
##
cor.test(res_stats_P[,'FC_AvB_P'], mergedStats[,'FC_AvB_P.Value'])
cor.test(res_stats_P[,'FC_AvC_P'], mergedStats[,'FC_AvC_P.Value'])
cor.test(res_stats_P[,'FC_BvC_P'], mergedStats[,'FC_BvC_P.Value'])
#
cor.test(res_stats_P[,'LA_AvB_P'], mergedStats[,'LA_AvB_P.Value'])
cor.test(res_stats_P[,'LA_AvC_P'], mergedStats[,'LA_AvC_P.Value'])
cor.test(res_stats_P[,'LA_BvC_P'], mergedStats[,'LA_BvC_P.Value'])
## FC ##
pdf('plots/Comparison_RMA_Model_Pvalues_TAC_vs_R.pdf', height=12, width=12)
par(mar=c(5,6,2,2))
plot(-log10(res_stats_P[,'FC_AvB_P']), -log10(mergedStats[,'FC_AvB_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: AvB" ,
xlim=c(0,5), ylim = c(0,5),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,5), y = c(0,5),col="red")
##
plot(-log10(res_stats_P[,'FC_AvC_P']), -log10(mergedStats[,'FC_AvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: AvC" ,
xlim=c(0,5), ylim = c(0,5),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,5), y = c(0,5),col="red")
##
plot(-log10(res_stats_P[,'FC_BvC_P']), -log10(mergedStats[,'FC_BvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: BvC" ,
xlim=c(0,5), ylim = c(0,5),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,5), y = c(0,5),col="red")
## LA ##
plot(-log10(res_stats_P[,'LA_AvB_P']), -log10(mergedStats[,'LA_AvB_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: AvB" ,
xlim=c(0,5), ylim = c(0,5),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,5), y = c(0,5),col="red")
##
plot(-log10(res_stats_P[,'LA_AvC_P']), -log10(mergedStats[,'LA_AvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: AvC" ,
xlim=c(0,5), ylim = c(0,5),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,5), y = c(0,5),col="red")
##
plot(-log10(res_stats_P[,'LA_BvC_P']), -log10(mergedStats[,'LA_BvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: BvC" ,
xlim=c(0,5), ylim = c(0,5),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,5), y = c(0,5),col="red")
dev.off()
#res_stats[[1]][match(rownames(mergedStats), res_stats[[1]][,'ID'] ),'ID'] == rownames(mergedStats)
################ Compare Full model RMA outputs ###########3
# Load R Stats
load('rda/FullModel_mergedStats_RMA_R.rda',verbose=T)
# Load TAC STats
load('TAC/RMA_BothRegion/MergedStats.rda',verbose=T) # res_stats
res_stats_P = sapply(res_stats, function(x) x[match(rownames(mergedStats) , x[,'ID']),'P-val'])
rownames(res_stats_P) = rownames(mergedStats)
colnames(res_stats_P) <- paste0(colnames(res_stats_P), "_P")
##
cor.test(res_stats_P[,'FC_AvB_P'], mergedStats[,'FC_AvB_P.Value'])
cor.test(res_stats_P[,'FC_AvC_P'], mergedStats[,'FC_AvC_P.Value'])
cor.test(res_stats_P[,'FC_BvC_P'], mergedStats[,'FC_BvC_P.Value'])
#
cor.test(res_stats_P[,'LA_AvB_P'], mergedStats[,'LA_AvB_P.Value'])
cor.test(res_stats_P[,'LA_AvC_P'], mergedStats[,'LA_AvC_P.Value'])
cor.test(res_stats_P[,'LA_BvC_P'], mergedStats[,'LA_BvC_P.Value'])
pdf('plots/FullModel_Comparison_RMA_Model_Pvalues_TAC_vs_R.pdf', height=12, width=12)
par(mar=c(5,6,2,2))
plot(-log10(res_stats_P[,'FC_AvB_P']), -log10(mergedStats[,'FC_AvB_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: AvB" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'FC_AvC_P']), -log10(mergedStats[,'FC_AvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: AvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'FC_BvC_P']), -log10(mergedStats[,'FC_BvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: BvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
## LA ##
plot(-log10(res_stats_P[,'LA_AvB_P']), -log10(mergedStats[,'LA_AvB_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: AvB" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'LA_AvC_P']), -log10(mergedStats[,'LA_AvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: AvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'LA_BvC_P']), -log10(mergedStats[,'LA_BvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: BvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
dev.off()
#res_stats[[1]][match(rownames(mergedStats), res_stats[[1]][,'ID'] ),'ID'] == rownames(mergedStats)
## Compare SST-RMA to RMA (both regions)
load('TAC/SST-RMA_BothRegions/MergedStats.rda')
res_stats_P = sapply(res_stats, function(x) x[match(rownames(mergedStats) , x[,'ID']),'P-val'])
rownames(res_stats_P) = rownames(mergedStats)
colnames(res_stats_P) <- paste0(colnames(res_stats_P), "_P")
colnames(res_stats_P) <- gsub("_v_", "v", colnames(res_stats_P) )
##
cor.test(res_stats_P[,'FC_AvB_P'], mergedStats[,'FC_AvB_P.Value'])
cor.test(res_stats_P[,'FC_AvC_P'], mergedStats[,'FC_AvC_P.Value'])
cor.test(res_stats_P[,'FC_BvC_P'], mergedStats[,'FC_BvC_P.Value'])
#
cor.test(res_stats_P[,'LA_AvB_P'], mergedStats[,'LA_AvB_P.Value'])
cor.test(res_stats_P[,'LA_AvC_P'], mergedStats[,'LA_AvC_P.Value'])
cor.test(res_stats_P[,'LA_BvC_P'], mergedStats[,'LA_BvC_P.Value'])
pdf('plots/FullModel_Comparison_SST-RMA_vs_RMA_Model_Pvalues_TAC_vs_R.pdf', height=12, width=12)
par(mar=c(5,6,2,2))
plot(-log10(res_stats_P[,'FC_AvB_P']), -log10(mergedStats[,'FC_AvB_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: AvB" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'FC_AvC_P']), -log10(mergedStats[,'FC_AvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: AvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'FC_BvC_P']), -log10(mergedStats[,'FC_BvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: BvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
## LA ##
plot(-log10(res_stats_P[,'LA_AvB_P']), -log10(mergedStats[,'LA_AvB_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: AvB" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'LA_AvC_P']), -log10(mergedStats[,'LA_AvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: AvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'LA_BvC_P']), -log10(mergedStats[,'LA_BvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: BvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
dev.off()
##### Compare log2 fold change between R RMA and TAC SST-RMA
res_stats_FC = sapply(res_stats, function(x) x[match(rownames(mergedStats) , x[,'ID']),'Fold Change'])
rownames(res_stats_FC) = rownames(mergedStats)
colnames(res_stats_FC) <- paste0(colnames(res_stats_FC), "_FC")
colnames(res_stats_FC) <- gsub("_v_", "v", colnames(res_stats_FC) )
res_stats_LFC = log2(abs(res_stats_FC))
##
cor.test(res_stats[[1]][match(rownames(mergedStats) , res_stats[[1]][,'ID']),'B Avg (log2)'] - res_stats[[1]][match(rownames(mergedStats) , res_stats[[1]][,'ID']),'A Avg (log2)'] , mergedStats[,'FC_AvB_logFC'])
cor.test(res_stats[[1]][match(rownames(mergedStats) , res_stats[[1]][,'ID']),'A Avg (log2)'] - res_stats[[1]][match(rownames(mergedStats) , res_stats[[1]][,'ID']),'B Avg (log2)'] , mergedStats[,'FC_AvB_logFC'])
plot(res_stats[[1]][match(rownames(mergedStats) , res_stats[[1]][,'ID']),'A Avg (log2)'] - res_stats[[1]][match(rownames(mergedStats) , res_stats[[1]][,'ID']),'B Avg (log2)'] , mergedStats[,'FC_AvB_logFC'])
cor.test(res_stats_FC[,'FC_AvB_FC'], 2^mergedStats[,'FC_AvB_logFC'])
plot(res_stats_FC[,'FC_AvB_FC'], 2^mergedStats[,'FC_AvB_logFC'])
cor.test(res_stats_FC[,'FC_AvC_FC'], 2^mergedStats[,'FC_AvC_logFC'])
cor.test(res_stats_FC[,'FC_BvC_FC'], 2^mergedStats[,'FC_BvC_logFC'])
#
cor.test(res_stats_P[,'LA_AvB_P'], mergedStats[,'LA_AvB_P.Value'])
cor.test(res_stats_P[,'LA_AvC_P'], mergedStats[,'LA_AvC_P.Value'])
cor.test(res_stats_P[,'LA_BvC_P'], mergedStats[,'LA_BvC_P.Value'])
pdf('plots/FullModel_Comparison_SST-RMA_vs_RMA_Model_Pvalues_TAC_vs_R.pdf', height=12, width=12)
par(mar=c(5,6,2,2))
plot(-log10(res_stats_P[,'FC_AvB_P']), -log10(mergedStats[,'FC_AvB_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: AvB" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'FC_AvC_P']), -log10(mergedStats[,'FC_AvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: AvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'FC_BvC_P']), -log10(mergedStats[,'FC_BvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="FC: BvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
## LA ##
plot(-log10(res_stats_P[,'LA_AvB_P']), -log10(mergedStats[,'LA_AvB_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: AvB" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'LA_AvC_P']), -log10(mergedStats[,'LA_AvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: AvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
##
plot(-log10(res_stats_P[,'LA_BvC_P']), -log10(mergedStats[,'LA_BvC_P.Value']), pch = 21, bg="grey",
xlab="-log10(P) [From TAC]", ylab="-log10(P) [From R]", main ="LA: BvC" ,
xlim=c(0,6), ylim = c(0,6),
cex.axis=2,cex.lab=2, cex.main=2)
lines(x = c(0,6), y = c(0,6),col="red")
dev.off()