Merge up and down

CNIC-Proteomics · Apr 9, 2024 · ff4afb1 · ff4afb1
1 parent 2ad5226
commit ff4afb1
Show file tree

Hide file tree

Showing 22 changed files with 313,307 additions and 8 deletions.
diff --git a/2_ReportLimma_wo_GUI_oneSample/B0/Z_p2qf/input.tsv b/2_ReportLimma_wo_GUI_oneSample/B0/Z_p2qf/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/B0/Z_pdm2pgm/input.tsv b/2_ReportLimma_wo_GUI_oneSample/B0/Z_pdm2pgm/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/B0/Z_pgm2p/input.tsv b/2_ReportLimma_wo_GUI_oneSample/B0/Z_pgm2p/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/B0/Z_pgm2p_dNM/input.tsv b/2_ReportLimma_wo_GUI_oneSample/B0/Z_pgm2p_dNM/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/B0/Z_q2all/input.tsv b/2_ReportLimma_wo_GUI_oneSample/B0/Z_q2all/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/B0/Z_qf2q/input.tsv b/2_ReportLimma_wo_GUI_oneSample/B0/Z_qf2q/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/F/Z_p2qf/input.tsv b/2_ReportLimma_wo_GUI_oneSample/F/Z_p2qf/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/F/Z_pdm2pgm/input.tsv b/2_ReportLimma_wo_GUI_oneSample/F/Z_pdm2pgm/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/F/Z_pgm2p/input.tsv b/2_ReportLimma_wo_GUI_oneSample/F/Z_pgm2p/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/F/Z_pgm2p_dNM/input.tsv b/2_ReportLimma_wo_GUI_oneSample/F/Z_pgm2p_dNM/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/F/Z_q2all/input.tsv b/2_ReportLimma_wo_GUI_oneSample/F/Z_q2all/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/F/Z_qf2q/input.tsv b/2_ReportLimma_wo_GUI_oneSample/F/Z_qf2q/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/I/Z_p2qf/input.tsv b/2_ReportLimma_wo_GUI_oneSample/I/Z_p2qf/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/I/Z_pdm2pgm/input.tsv b/2_ReportLimma_wo_GUI_oneSample/I/Z_pdm2pgm/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/I/Z_pgm2p/input.tsv b/2_ReportLimma_wo_GUI_oneSample/I/Z_pgm2p/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/I/Z_pgm2p_dNM/input.tsv b/2_ReportLimma_wo_GUI_oneSample/I/Z_pgm2p_dNM/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/I/Z_q2all/input.tsv b/2_ReportLimma_wo_GUI_oneSample/I/Z_q2all/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/I/Z_qf2q/input.tsv b/2_ReportLimma_wo_GUI_oneSample/I/Z_qf2q/input.tsv
diff --git a/2_ReportLimma_wo_GUI_oneSample/oneSampleLimma.R b/2_ReportLimma_wo_GUI_oneSample/oneSampleLimma.R
@@ -0,0 +1,42 @@
+library(limma)
+
+'
+https://bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf
+16.1 Swirl Zebrafish: A Single-Group Experiment
+pg. 76
+'
+
+setwd("S:\\U_Proteomica\\LABS\\LAB_DF\\Comet_PTM\\FA_Biopsias\\2_ReportLimma_wo_GUI_oneSample")
+
+groups <- c('B0', 'F', 'I')
+integrations <- c('Z_pdm2pgm', 'Z_pgm2p', 'Z_pgm2p_dNM', 'Z_p2qf', 'Z_qf2q', 'Z_q2all')
+
+intgr <- integrations[1]
+
+for (g in groups) {
+
+
+  for (intgr in integrations) {
+
+    df <- read.csv(paste0(g, "\\", intgr, "\\", "input.tsv"), header=T, sep="\t")
+    rownames(df) <- df$LEVEL
+    df$LEVEL <- NULL
+
+    samples <- colnames(df)
+    design <- matrix(rep(1, length(samples)))
+    rownames(design) <- samples
+    colnames(design) <- g
+
+    fit <- lmFit(df,design)
+    fit <- eBayes(fit)
+
+    pvalue <- as.data.frame(fit$p.value)
+    meanRow <- as.data.frame(fit$Amean)
+
+    output <- merge(meanRow, pvalue, 'row.names', all=T)
+    colnames(output) <- c('LEVEL', 'Mean', 'pvalue')
+
+    write.table(output, paste0(g, "\\", intgr, "\\", "output.tsv"), sep="\t", row.names=F, col.names=T)
+
+  }
+}