10.6084/m9.figshare.c.3645239_D4.v1 Jason Gerstner Jason Gerstner John Koberstein John Koberstein Adam Watson Adam Watson Nikolai Zapero Nikolai Zapero Davide Risso Davide Risso Terence Speed Terence Speed Marcos Frank Marcos Frank Lucia Peixoto Lucia Peixoto Additional file 3: of Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex Springer Nature 2016 Sleep Sleep deprivation Circadian Microarray Gene mRNA Transcriptomics 2016-10-25 05:00:00 Journal contribution https://springernature.figshare.com/articles/journal_contribution/Additional_file_3_of_Removal_of_unwanted_variation_reveals_novel_patterns_of_gene_expression_linked_to_sleep_homeostasis_in_murine_cortex/4471337 Impact of RUV on differential expression. A) Top left. Distribution of unadjusted limma p-values for tests of differential expression between SD and CC samples following RMA and RUV normalization. RUV increases discovery of differentially expressed genes (genes that have a low p-value). Bottom. Volcano plot of differential expression (竏値og10 p-value vs log fold change) of Quantile and RUV normalized samples. Genes with and FDR <0.01 are highlighted in blue. Positive controls are circled in red. B) Top right. Distribution of unadjusted limma p-values for tests of differential expression between RS2 and CC samples following RMA and RUV normalization. RUV increases discovery of differentially expressed genes (genes that have a low p-value). Bottom. Volcano plot of differential expression (竏値og10 p-value vs log fold change) of Quantile and RUV normalized samples. Genes with and FDR <0.01 are highlighted in blue. Positive controls are circled in red. C) Bottom left. Distribution of unadjusted limma p-values for tests of differential expression between RS3 and CC samples following RMA and RUV normalization. RUV increases discovery of differentially expressed genes (genes that have a low p-value). Bottom. Volcano plot of differential expression (竏値og10 p-value vs log fold change) of Quantile and RUV normalized samples. Genes with and FDR <0.01 are highlighted in blue. Positive controls are circled in red. D) Bottom right. Distribution of unadjusted limma p-values for tests of differential expression between RS6 and CC samples following RMA and RUV normalization. RUV increases discovery of differentially expressed genes (genes that have a low p-value). Bottom. Volcano plot of differential expression (竏値og10 p-value vs log fold change) of Quantile and RUV normalized samples. Genes with and FDR <0.01 are highlighted in blue. Positive controls are circled in red. (PDF 6414 kb)