The function compares time dependent behaviour of genes in two different groups. Applying empirical Bayes moderate F-statistic on differences in coefficients of fitted natural cubic spline regression models, differentially expressed in time genes are determined. The function is a wrapper of other R-functions to simplify differential expression analysis of time-course data.
number of degrees of freedom
Benjamini-Hochberg adjusted p-value cut-off
character defining which treatment group should be considered as reference
The function fits a temporal trend using a natural cubic spline regression to simulate nonlinear behaviour of genes over time.
eSetObject must be provided as an object of class
ExpressionSet which contains
Treatment and if applicable
Replicates variables (columns) included in the phenotypic data of the
pData(eSetObject)). Two types of
Treatment defining two groups to compare have to be definied.
Replicates are not required. The time points for compared treatment groups should be identical.
User has to define number of degrees of freedom (
df) for the spline regression model. Choosing effective degrees of freedom in range 3-5 is reasonable.
Time dependent differential expression of a gene is determined by the application of empirical Bayes moderate F-statistics on the differences of coefficient values of the fitted natural cubic spline regression models for the same gene in the two compared treatment groups. In other words, comparing the coefficient values of the fitted splines in both groups allows the detection of differences in the shape of the curves, which represent the gene expressions changes over time. Ouptut table containing Benjamini-Hochberg adjusted p-value (
adj.P.Value) is used to define differentially expressed genes. The default value for
cutoff.adj.pVal is set to
1, which means that all genes are included in output table.
A data.frame with rows defining names/IDs of differentially expressed genes and additional columns described below.
The first columns contain all feature data of the
fData(eSetObject)), if any feature data were defined. Otherwise, only one column
row_IDs, containing the row names is created. The
b_m coefficients correspond to the reference model parameters. The
d_m coefficients represent the differences between the reference model parameters and the model parameters in the compared group.
AveExprs refers to the average log2-expression for a probe (representing a gene) over all arrays. The
F column contains moderate F-statistics,
P.Value raw p-value and
adj.P.Value Benjamini-Hochberg adjusted p-value.
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## load "eSetObject" containing simulated time-course data data(TCsimData) pData(TCsimData) ## define function parameters df <- 3 cutoff.adj.pVal <- 0.01 reference <- "T1" intercept <- TRUE diffExprs <- splineDiffExprs(eSetObject = TCsimData, df, cutoff.adj.pVal, reference, intercept) head(diffExprs,3)
Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: igraph Attaching package: 'igraph' The following objects are masked from 'package:BiocGenerics': normalize, path, union The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: GSEABase Loading required package: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode The following objects are masked from 'package:igraph': degree, edges, intersection Loading required package: gtools Attaching package: 'gtools' The following object is masked from 'package:igraph': permute Loading required package: splines Loading required package: GeneNet Loading required package: corpcor Loading required package: longitudinal Loading required package: fdrtool Loading required package: FIs SampleName Time Treatment Replicate 1 T1_1_A 1 T1 A 2 T1_4_A 4 T1 A 3 T1_8_A 8 T1 A 4 T1_16_A 16 T1 A 5 T1_24_A 24 T1 A 6 T1_32_A 32 T1 A 7 T1_40_A 40 T1 A 8 T1_48_A 48 T1 A 9 T1_1_B 1 T1 B 10 T1_4_B 4 T1 B 11 T1_8_B 8 T1 B 12 T1_16_B 16 T1 B 13 T1_24_B 24 T1 B 14 T1_32_B 32 T1 B 15 T1_40_B 40 T1 B 16 T1_48_B 48 T1 B 17 T2_1_A 1 T2 A 18 T2_4_A 4 T2 A 19 T2_8_A 8 T2 A 20 T2_16_A 16 T2 A 21 T2_24_A 24 T2 A 22 T2_32_A 32 T2 A 23 T2_40_A 40 T2 A 24 T2_48_A 48 T2 A 25 T2_1_B 1 T2 B 26 T2_4_B 4 T2 B 27 T2_8_B 8 T2 B 28 T2_16_B 16 T2 B 29 T2_24_B 24 T2 B 30 T2_32_B 32 T2 B 31 T2_40_B 40 T2 B 32 T2_48_B 48 T2 B ------------------------------------------------- Differential analysis done for df = 3 and adj.P.Val <= 0.01 Number of differentially expressed genes: 952 row_IDs b_0 b_1 b_2 b_3 d_0 BRAF BRAF 0.2248186 -0.06672491 -0.11466685 -0.01113329 0.04537218 EEF2 EEF2 0.1662325 0.03093095 0.02415684 0.05805703 0.04218390 OR5W2 OR5W2 0.5600514 -0.11141556 -0.26764248 0.13582290 0.10798569 d_1 d_2 d_3 AveExpr F P.Value BRAF 0.09884069 0.32667028 0.1362235 0.2616200 100.47655 8.552316e-19 EEF2 0.03907564 0.36776057 0.1663112 0.2632523 75.34076 8.442937e-17 OR5W2 0.29355341 0.08948516 -0.1577280 0.5454758 71.98754 1.723753e-16 adj.P.Val BRAF 1.710463e-15 EEF2 8.442937e-14 OR5W2 1.149169e-13
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