Author: Josset, Laurence; Zeng, Hui; Kelly, Sara M.; Tumpey, Terrence M.; Katze, Michael G.
Title: Transcriptomic Characterization of the Novel Avian-Origin Influenza A (H7N9) Virus: Specific Host Response and Responses Intermediate between Avian (H5N1 and H7N7) and Human (H3N2) Viruses and Implications for Treatment Options Document date: 2014_2_4
ID: uz0m1o0q_27
Snippet: Statistical analysis. Differential expression was determined by comparing IAV-infected replicates to time-matched mocks, based on a linear model fit for each probe using the R software package "limma" (42) . Criteria for differential expression were an absolute log 2 FC of 1.5 and a q value of Ͻ0.01 calculated using a moderated t test with subsequent Benjamini-Hochberg correction. This controls the false discovery rate (FDR) associated with our .....
Document: Statistical analysis. Differential expression was determined by comparing IAV-infected replicates to time-matched mocks, based on a linear model fit for each probe using the R software package "limma" (42) . Criteria for differential expression were an absolute log 2 FC of 1.5 and a q value of Ͻ0.01 calculated using a moderated t test with subsequent Benjamini-Hochberg correction. This controls the false discovery rate (FDR) associated with our results to 1%. For each viral condition, genes were classified as up-or downregulated throughout infection if they were found significantly up-or downregulated at at least one time point. Genes that were found to be both up-and downregulated at different time points were classified as genes with transient expression. A binary DE matrix with 3 columns per viral treatment (gene up-or downregulated or transient genes) and values equal to 1 for DE and 0 for not DE was used to cluster DE genes in 25 clusters by Euclidian distance and constant height cut of a hierarchical clustering dendrogram (43) .
Search related documents:
Co phrase search for related documents- discovery rate and FDR false discovery rate: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70
- discovery rate and linear model: 1, 2, 3
- discovery rate and statistical analysis: 1, 2, 3, 4, 5, 6, 7
- discovery rate and time match: 1
- discovery rate and time point: 1, 2
- euclidian distance and time point: 1, 2
- euclidian distance and viral condition: 1
- euclidian distance and viral treatment: 1, 2
- false discovery rate and FDR false discovery rate: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70
- false discovery rate and linear model: 1, 2, 3
- false discovery rate and statistical analysis: 1, 2, 3, 4, 5
- false discovery rate and time match: 1
- false discovery rate and time point: 1, 2
- FDR false discovery rate and statistical analysis: 1, 2
- FDR false discovery rate and time match: 1
- FDR false discovery rate and time point: 1, 2
- gene classify and linear model: 1
- statistical analysis and time point: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24
- statistical analysis and viral treatment: 1, 2, 3
Co phrase search for related documents, hyperlinks ordered by date