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)