Differentially expressed gene lists:

Click on the hyperlinks to see the results.
FileName Description
ANOVA.ls ANOVA MODEL (all genes and samples, least squares), log2 fold change for all groups, genes with F-statistics > 90th percentile
ANOVA.rb ANOVA MODEL (all genes and samples, robust), log2 fold change for all groups, genes with F-statistics > 90th percentile
AzaC_TSAvsControl.ls ANOVA MODEL (all genes and samples, least squares), AzaC_TSAvsControl contrast: AzaC + TSA vs. Control cell lines, genes with B-statistics > 90th percentile
AzaC_TSAvsControl.rb ANOVA MODEL (all genes and samples, robust), AzaC_TSAvsControl contrast: AzaC + TSA vs. Control cell lines, genes with B-statistics > 90th percentile
AzaCvsControl.ls ANOVA MODEL (all genes and samples, least squares), AzaCvsControl contrast: AzaC vs. Control cell lines, genes with B-statistics > 90th percentile
AzaCvsControl.rb ANOVA MODEL (all genes and samples, robust), AzaCvsControl contrast: AzaC vs. Control cell lines, genes with B-statistics > 90th percentile
TSAvsControl.ls ANOVA MODEL (all genes and samples, least squares), TSAvsControl contrast: TSA vs. Control cell lines, genes with B-statistics > 90th percentile
TSAvsControl.rb ANOVA MODEL (all genes and samples, robust), TSAvsControl contrast: TSA vs. Control cell lines, genes with B-statistics > 90th percentile

Diagnostics and results figures:

Click on the hyperlinks to see the results.
FileName Description
bxpexp Boxplot for Log2 expression before and after Loess and Rquantile normalization
bxpMval Boxplot for M values (compared to the median array) before and after Loess and Rquantile normalization
bxpAval Boxplot for A values (compared to the median array) before and after Loess and Rquantile normalization
MAplots MAplots for each array, raw data
MAnQplots MAplots for each array, after Loess and Rquantile normalization
expIntQuDiff Interquartile differences of Log2 expression before and after Loess and Rquantile Rnormalization
expMedian Medians of Log2 expression before and after Loess and Rquantile normalization
corrHM.RG Samples pair-wise correlation heatmap, raw data
corrHM.RGnQ Samples pair-wise correlation heatmap, Loess and Rquantile normalized data
qqPlots.ls QQ-plot for each contrast (least squares method)
qqPlots.rb QQ-plot for each contrast (robust method)
contrasts.BvsM.ls Volcano plots for each performed comparison (least squares method)
contrasts.BvsM.rb Volcano plots for each performed comparison (robust method)
contrasts.MAplot.ls MAplots for each performed comparison (least squares method)
contrasts.MAplot.rb MAplots for each performed comparison (robust method)