# GeneRatio BgRatio pvalue p.adjust qvalue # DOID:1882 DOID:1882 atrial heart septal defect # DOID:2348 DOID:2348 arteriosclerotic cardiovascular disease # DOID:17 DOID:17 musculoskeletal system disease # DOID:3342 DOID:3342 bone inflammation disease # DOID:9008 DOID:9008 psoriatic arthritis Sig.genes = gettext(aafLocusLink(as.character($probeID), 'hugene10sttranscriptcluster.db')) # annot.outputs = annot.outputĭOSE: Disease Ontology Semantic and Enrichment Analysis library(DOSE)

# annot.output = read.table(file = '', header = T, sep = ' ', nrows = 7) # Print top 7 significant genes at p ≤ 0.01 level # Export results to an HTML and text file # Add the 'AdjpValue' and 'FoldChange' variables to the annotation tableĪtable = aafTable(`P-Value` = $AdjpValue, signed = TRUE)įCtable = aafTable(`Fold Change` = $FoldChange, signed = TRUE) # Annotate the top 250 significant genesĪnntable = aafTableAnn(as.character($probeID), 'hugene10sttranscriptcluster.db') # Load annaffy and hugene10sttranscriptcluster.db libraries Input cluster analysis output from DAVID and print the first three rows options(width = 500) Size = 1.75) + labs(title = 'PAH Volcano Plot') + xlim(c(-2, 2)) + ylim(c(0,Ģ)) + xlab('Log2 Fold Change') + ylab('-Log10 P-Values')Īnnotate the top 250 significant genes, output to a text file. Y = -log10($AdjpValue)), colour = none) + geom_point(alpha = 0.4, Volcano = ggplot(data =, aes(x = log2($FoldChange), Head() # probeID Stat RawpValue AdjpValue FoldChange = merge(, FC.raw, by = 'probeID', all.y = TRUE, # Merge the 'FoldChange' Variable into database by probeID # Extract the 'probeID' and 'FoldChange' variables from the įC.raw = ' head(PUBHI.SAM) # probeID Stat RawpValue FoldChange Significant # We're doing 24310 complete permutations Q = 0.2, plot = FALSE) # 'typeFDR= FDR-BH' head(PUBHI.ttest) # probeID Stat RawpValue AdjpValue PUBHI.ttest = runTtest(combat_edata, labels =, algo = 't.equalvar', # Run Student's t-test with batch corrected data Merge the test results into one data set to produce a heatmap # Set-up Student's t-test comparison factor Run Student’s t-test and Significance of Analysis of Microarrays (SAM) test on normalized data. PHBI.norm = rma(PHBI.data) # Background correcting PHBI.data = read.celfiles(PHBI.CEL) # Reading in.

PHBI.CEL = paste('./data/', PHBI.CEL, sep = '') Import Raw Data and Normalization library('pd.hugene.1.0.st.v1') = read.table(file = './data/PHBI cel annotation BIO6660 v2.txt', header = T, First we will import a file PHBI cel annotation BIO6660 v2.txt that contains experimental info pertaining to the dataset.

Microarray probe to gene r taply