make.design.matrix: Make a design matrix for regression fit of time series gene...
In maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
make.design.matrix creates the design matrix of dummies for fitting time series micorarray
gene expression experiments.
Usage
1
2
make.design.matrix(edesign, degree = 2, time.col = 1,
repl.col = 2, group.cols = c(3:ncol(edesign)))
Arguments
edesign
matrix describing experimental design. Rows must be arrays and columns experiment descriptors
degree
the degree of the regression fit polynome. degree = 1 returns linear regression, degree = 2 returns quadratic regression, etc
time.col
column number in edesign containing time values. Default is first column
repl.col
column number in edesign containing coding for replicate arrays. Default is second column
group.cols
column numbers in edesign indicating the coding for each experimental group (treatment, tissue, ...). See details
Details
rownames of edesign object should contain the arrays naming (i.e. array1, array2, ...).
colnames of edesign must contain the names of experiment descriptors(i.e. "Time", "Replicates", "Treatment A", "Treatment B", etc.).
for each experimental group a different column must be present in edesign, coding with 1 and 0 whether each array belongs to that group or not.
make.design.matrix returns a design matrix where rows represent arrays and column variables of time, dummies and their interactions for up to the degree given.
Dummies show the relative effect of each experimental group related to the first one. Single dummies indicate the abcissa component of each group.
$Time*dummy$ variables indicate slope changes, $Time^2*dummy$ indicates curvature changes. Higher grade values could model complex responses.
In case experimental groups share a initial state (i.e. common time 0), no single dummies are modeled.
Value
dis
design matrix of dummies for fitting time series
groups.vector
vector coding the experimental group to which each variable belongs to
edesign
edesign value passed as argument
Author(s)
Ana Conesa, aconesa@cipf.es; Maria Jose Nueda, mj.nueda@ua.es
References
Conesa, A., Nueda M.J., Alberto Ferrer, A., Talon, T. 2006.
maSigPro: a Method to Identify Significant Differential Expression Profiles in Time-Course Microarray Experiments.
Bioinformatics 22, 1096-1102
Examples
1
2
3
data(edesign.abiotic, edesignCT)
make.design.matrix(edesign.abiotic) # quadratic model
make.design.matrix(edesignCT, degree = 3) # cubic model with common starting time point
Example output
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, cbind, colMeans, colSums, colnames, 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: MASS
$dis
ColdvsControl HeatvsControl SaltvsControl Time TimexCold
Control_3H_1 0 0 0 3 0
Control_3H_2 0 0 0 3 0
Control_3H_3 0 0 0 3 0
Control_9H_1 0 0 0 9 0
Control_9H_2 0 0 0 9 0
Control_9H_3 0 0 0 9 0
Control_27H_1 0 0 0 27 0
Control_27H_2 0 0 0 27 0
Control_27H_3 0 0 0 27 0
Cold_3H_1 1 0 0 3 3
Cold_3H_2 1 0 0 3 3
Cold_3H_3 1 0 0 3 3
Cold_9H_1 1 0 0 9 9
Cold_9H_2 1 0 0 9 9
Cold_9H_3 1 0 0 9 9
Cold_27H_1 1 0 0 27 27
Cold_27H_2 1 0 0 27 27
Cold_27H_3 1 0 0 27 27
Heat_3H_1 0 1 0 3 0
Heat_3H_2 0 1 0 3 0
Heat_3H_3 0 1 0 3 0
Heat_9H_1 0 1 0 9 0
Heat_9H_2 0 1 0 9 0
Heat_9H_3 0 1 0 9 0
Heat_27H_1 0 1 0 27 0
Heat_27H_2 0 1 0 27 0
Heat_27H_3 0 1 0 27 0
Salt_3H_1 0 0 1 3 0
Salt_3H_2 0 0 1 3 0
Salt_3H_3 0 0 1 3 0
Salt_9H_1 0 0 1 9 0
Salt_9H_2 0 0 1 9 0
Salt_9H_3 0 0 1 9 0
Salt_27H_1 0 0 1 27 0
Salt_27H_2 0 0 1 27 0
Salt_27H_3 0 0 1 27 0
TimexHeat TimexSalt Time2 Time2xCold Time2xHeat Time2xSalt
Control_3H_1 0 0 9 0 0 0
Control_3H_2 0 0 9 0 0 0
Control_3H_3 0 0 9 0 0 0
Control_9H_1 0 0 81 0 0 0
Control_9H_2 0 0 81 0 0 0
Control_9H_3 0 0 81 0 0 0
Control_27H_1 0 0 729 0 0 0
Control_27H_2 0 0 729 0 0 0
Control_27H_3 0 0 729 0 0 0
Cold_3H_1 0 0 9 9 0 0
Cold_3H_2 0 0 9 9 0 0
Cold_3H_3 0 0 9 9 0 0
Cold_9H_1 0 0 81 81 0 0
Cold_9H_2 0 0 81 81 0 0
Cold_9H_3 0 0 81 81 0 0
Cold_27H_1 0 0 729 729 0 0
Cold_27H_2 0 0 729 729 0 0
Cold_27H_3 0 0 729 729 0 0
Heat_3H_1 3 0 9 0 9 0
Heat_3H_2 3 0 9 0 9 0
Heat_3H_3 3 0 9 0 9 0
Heat_9H_1 9 0 81 0 81 0
Heat_9H_2 9 0 81 0 81 0
Heat_9H_3 9 0 81 0 81 0
Heat_27H_1 27 0 729 0 729 0
Heat_27H_2 27 0 729 0 729 0
Heat_27H_3 27 0 729 0 729 0
Salt_3H_1 0 3 9 0 0 9
Salt_3H_2 0 3 9 0 0 9
Salt_3H_3 0 3 9 0 0 9
Salt_9H_1 0 9 81 0 0 81
Salt_9H_2 0 9 81 0 0 81
Salt_9H_3 0 9 81 0 0 81
Salt_27H_1 0 27 729 0 0 729
Salt_27H_2 0 27 729 0 0 729
Salt_27H_3 0 27 729 0 0 729
$groups.vector
[1] "ColdvsControl" "HeatvsControl" "SaltvsControl" "Control"
[5] "ColdvsControl" "HeatvsControl" "SaltvsControl" "Control"
[9] "ColdvsControl" "HeatvsControl" "SaltvsControl"
$edesign
Time Replicate Control Cold Heat Salt
Control_3H_1 3 1 1 0 0 0
Control_3H_2 3 1 1 0 0 0
Control_3H_3 3 1 1 0 0 0
Control_9H_1 9 2 1 0 0 0
Control_9H_2 9 2 1 0 0 0
Control_9H_3 9 2 1 0 0 0
Control_27H_1 27 3 1 0 0 0
Control_27H_2 27 3 1 0 0 0
Control_27H_3 27 3 1 0 0 0
Cold_3H_1 3 4 0 1 0 0
Cold_3H_2 3 4 0 1 0 0
Cold_3H_3 3 4 0 1 0 0
Cold_9H_1 9 5 0 1 0 0
Cold_9H_2 9 5 0 1 0 0
Cold_9H_3 9 5 0 1 0 0
Cold_27H_1 27 6 0 1 0 0
Cold_27H_2 27 6 0 1 0 0
Cold_27H_3 27 6 0 1 0 0
Heat_3H_1 3 7 0 0 1 0
Heat_3H_2 3 7 0 0 1 0
Heat_3H_3 3 7 0 0 1 0
Heat_9H_1 9 8 0 0 1 0
Heat_9H_2 9 8 0 0 1 0
Heat_9H_3 9 8 0 0 1 0
Heat_27H_1 27 9 0 0 1 0
Heat_27H_2 27 9 0 0 1 0
Heat_27H_3 27 9 0 0 1 0
Salt_3H_1 3 10 0 0 0 1
Salt_3H_2 3 10 0 0 0 1
Salt_3H_3 3 10 0 0 0 1
Salt_9H_1 9 11 0 0 0 1
Salt_9H_2 9 11 0 0 0 1
Salt_9H_3 9 11 0 0 0 1
Salt_27H_1 27 12 0 0 0 1
Salt_27H_2 27 12 0 0 0 1
Salt_27H_3 27 12 0 0 0 1
$dis
Time TimexTissue1 TimexTissue2 TimexTissue3 TimexTissue4 Time2
Array1 0 0 0 0 0 0
Array2 0 0 0 0 0 0
Array3 2 2 0 0 0 4
Array4 2 2 0 0 0 4
Array5 2 0 0 2 0 4
Array6 2 0 0 2 0 4
Array7 2 0 0 0 0 4
Array8 2 0 0 0 0 4
Array9 2 0 2 0 0 4
Array10 2 0 2 0 0 4
Array11 2 0 0 0 2 4
Array12 2 0 0 0 2 4
Array13 4 4 0 0 0 16
Array14 4 4 0 0 0 16
Array15 4 0 0 4 0 16
Array16 4 0 0 4 0 16
Array17 4 0 0 0 0 16
Array18 4 0 0 0 0 16
Array19 4 0 4 0 0 16
Array20 4 0 4 0 0 16
Array21 4 0 0 0 4 16
Array22 4 0 0 0 4 16
Array23 6 6 0 0 0 36
Array24 6 6 0 0 0 36
Array25 6 0 0 6 0 36
Array26 6 0 0 6 0 36
Array27 6 0 0 0 0 36
Array28 6 0 0 0 0 36
Array29 6 0 6 0 0 36
Array30 6 0 6 0 0 36
Array31 6 0 0 0 6 36
Array32 6 0 0 0 6 36
Time2xTissue1 Time2xTissue2 Time2xTissue3 Time2xTissue4 Time3
Array1 0 0 0 0 0
Array2 0 0 0 0 0
Array3 4 0 0 0 8
Array4 4 0 0 0 8
Array5 0 0 4 0 8
Array6 0 0 4 0 8
Array7 0 0 0 0 8
Array8 0 0 0 0 8
Array9 0 4 0 0 8
Array10 0 4 0 0 8
Array11 0 0 0 4 8
Array12 0 0 0 4 8
Array13 16 0 0 0 64
Array14 16 0 0 0 64
Array15 0 0 16 0 64
Array16 0 0 16 0 64
Array17 0 0 0 0 64
Array18 0 0 0 0 64
Array19 0 16 0 0 64
Array20 0 16 0 0 64
Array21 0 0 0 16 64
Array22 0 0 0 16 64
Array23 36 0 0 0 216
Array24 36 0 0 0 216
Array25 0 0 36 0 216
Array26 0 0 36 0 216
Array27 0 0 0 0 216
Array28 0 0 0 0 216
Array29 0 36 0 0 216
Array30 0 36 0 0 216
Array31 0 0 0 36 216
Array32 0 0 0 36 216
Time3xTissue1 Time3xTissue2 Time3xTissue3 Time3xTissue4
Array1 0 0 0 0
Array2 0 0 0 0
Array3 8 0 0 0
Array4 8 0 0 0
Array5 0 0 8 0
Array6 0 0 8 0
Array7 0 0 0 0
Array8 0 0 0 0
Array9 0 8 0 0
Array10 0 8 0 0
Array11 0 0 0 8
Array12 0 0 0 8
Array13 64 0 0 0
Array14 64 0 0 0
Array15 0 0 64 0
Array16 0 0 64 0
Array17 0 0 0 0
Array18 0 0 0 0
Array19 0 64 0 0
Array20 0 64 0 0
Array21 0 0 0 64
Array22 0 0 0 64
Array23 216 0 0 0
Array24 216 0 0 0
Array25 0 0 216 0
Array26 0 0 216 0
Array27 0 0 0 0
Array28 0 0 0 0
Array29 0 216 0 0
Array30 0 216 0 0
Array31 0 0 0 216
Array32 0 0 0 216
$groups.vector
[1] "Control" "Tissue1vsControl" "Tissue2vsControl" "Tissue3vsControl"
[5] "Tissue4vsControl" "Control" "Tissue1vsControl" "Tissue2vsControl"
[9] "Tissue3vsControl" "Tissue4vsControl" "Control" "Tissue1vsControl"
[13] "Tissue2vsControl" "Tissue3vsControl" "Tissue4vsControl"
$edesign
Time Replicates Control Tissue1 Tissue2 Tissue3 Tissue4
Array1 0 1 1 1 1 1 1
Array2 0 1 1 1 1 1 1
Array3 2 2 0 1 0 0 0
Array4 2 2 0 1 0 0 0
Array5 2 3 0 0 0 1 0
Array6 2 3 0 0 0 1 0
Array7 2 4 1 0 0 0 0
Array8 2 4 1 0 0 0 0
Array9 2 5 0 0 1 0 0
Array10 2 5 0 0 1 0 0
Array11 2 6 0 0 0 0 1
Array12 2 6 0 0 0 0 1
Array13 4 7 0 1 0 0 0
Array14 4 7 0 1 0 0 0
Array15 4 8 0 0 0 1 0
Array16 4 8 0 0 0 1 0
Array17 4 9 1 0 0 0 0
Array18 4 9 1 0 0 0 0
Array19 4 10 0 0 1 0 0
Array20 4 10 0 0 1 0 0
Array21 4 11 0 0 0 0 1
Array22 4 11 0 0 0 0 1
Array23 6 12 0 1 0 0 0
Array24 6 12 0 1 0 0 0
Array25 6 13 0 0 0 1 0
Array26 6 13 0 0 0 1 0
Array27 6 14 1 0 0 0 0
Array28 6 14 1 0 0 0 0
Array29 6 15 0 0 1 0 0
Array30 6 15 0 0 1 0 0
Array31 6 16 0 0 0 0 1
Array32 6 16 0 0 0 0 1
maSigPro documentation built on Nov. 8, 2020, 6:51 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) References Examples
Description
make.design.matrix creates the design matrix of dummies for fitting time series micorarray
gene expression experiments.
Usage
1 2 | make.design.matrix(edesign, degree = 2, time.col = 1,
repl.col = 2, group.cols = c(3:ncol(edesign)))
|
Arguments
edesign |
matrix describing experimental design. Rows must be arrays and columns experiment descriptors |
degree |
the degree of the regression fit polynome. |
time.col |
column number in edesign containing time values. Default is first column |
repl.col |
column number in edesign containing coding for replicate arrays. Default is second column |
group.cols |
column numbers in edesign indicating the coding for each experimental group (treatment, tissue, ...). See details |
Details
rownames of edesign object should contain the arrays naming (i.e. array1, array2, ...). colnames of edesign must contain the names of experiment descriptors(i.e. "Time", "Replicates", "Treatment A", "Treatment B", etc.). for each experimental group a different column must be present in edesign, coding with 1 and 0 whether each array belongs to that group or not.
make.design.matrix returns a design matrix where rows represent arrays and column variables of time, dummies and their interactions for up to the degree given.
Dummies show the relative effect of each experimental group related to the first one. Single dummies indicate the abcissa component of each group.
$Time*dummy$ variables indicate slope changes, $Time^2*dummy$ indicates curvature changes. Higher grade values could model complex responses.
In case experimental groups share a initial state (i.e. common time 0), no single dummies are modeled.
Value
dis |
design matrix of dummies for fitting time series |
groups.vector |
vector coding the experimental group to which each variable belongs to |
edesign |
|
Author(s)
Ana Conesa, aconesa@cipf.es; Maria Jose Nueda, mj.nueda@ua.es
References
Conesa, A., Nueda M.J., Alberto Ferrer, A., Talon, T. 2006. maSigPro: a Method to Identify Significant Differential Expression Profiles in Time-Course Microarray Experiments. Bioinformatics 22, 1096-1102
Examples
1 2 3 | data(edesign.abiotic, edesignCT)
make.design.matrix(edesign.abiotic) # quadratic model
make.design.matrix(edesignCT, degree = 3) # cubic model with common starting time point
|
Example output
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, cbind, colMeans, colSums, colnames, 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: MASS
$dis
ColdvsControl HeatvsControl SaltvsControl Time TimexCold
Control_3H_1 0 0 0 3 0
Control_3H_2 0 0 0 3 0
Control_3H_3 0 0 0 3 0
Control_9H_1 0 0 0 9 0
Control_9H_2 0 0 0 9 0
Control_9H_3 0 0 0 9 0
Control_27H_1 0 0 0 27 0
Control_27H_2 0 0 0 27 0
Control_27H_3 0 0 0 27 0
Cold_3H_1 1 0 0 3 3
Cold_3H_2 1 0 0 3 3
Cold_3H_3 1 0 0 3 3
Cold_9H_1 1 0 0 9 9
Cold_9H_2 1 0 0 9 9
Cold_9H_3 1 0 0 9 9
Cold_27H_1 1 0 0 27 27
Cold_27H_2 1 0 0 27 27
Cold_27H_3 1 0 0 27 27
Heat_3H_1 0 1 0 3 0
Heat_3H_2 0 1 0 3 0
Heat_3H_3 0 1 0 3 0
Heat_9H_1 0 1 0 9 0
Heat_9H_2 0 1 0 9 0
Heat_9H_3 0 1 0 9 0
Heat_27H_1 0 1 0 27 0
Heat_27H_2 0 1 0 27 0
Heat_27H_3 0 1 0 27 0
Salt_3H_1 0 0 1 3 0
Salt_3H_2 0 0 1 3 0
Salt_3H_3 0 0 1 3 0
Salt_9H_1 0 0 1 9 0
Salt_9H_2 0 0 1 9 0
Salt_9H_3 0 0 1 9 0
Salt_27H_1 0 0 1 27 0
Salt_27H_2 0 0 1 27 0
Salt_27H_3 0 0 1 27 0
TimexHeat TimexSalt Time2 Time2xCold Time2xHeat Time2xSalt
Control_3H_1 0 0 9 0 0 0
Control_3H_2 0 0 9 0 0 0
Control_3H_3 0 0 9 0 0 0
Control_9H_1 0 0 81 0 0 0
Control_9H_2 0 0 81 0 0 0
Control_9H_3 0 0 81 0 0 0
Control_27H_1 0 0 729 0 0 0
Control_27H_2 0 0 729 0 0 0
Control_27H_3 0 0 729 0 0 0
Cold_3H_1 0 0 9 9 0 0
Cold_3H_2 0 0 9 9 0 0
Cold_3H_3 0 0 9 9 0 0
Cold_9H_1 0 0 81 81 0 0
Cold_9H_2 0 0 81 81 0 0
Cold_9H_3 0 0 81 81 0 0
Cold_27H_1 0 0 729 729 0 0
Cold_27H_2 0 0 729 729 0 0
Cold_27H_3 0 0 729 729 0 0
Heat_3H_1 3 0 9 0 9 0
Heat_3H_2 3 0 9 0 9 0
Heat_3H_3 3 0 9 0 9 0
Heat_9H_1 9 0 81 0 81 0
Heat_9H_2 9 0 81 0 81 0
Heat_9H_3 9 0 81 0 81 0
Heat_27H_1 27 0 729 0 729 0
Heat_27H_2 27 0 729 0 729 0
Heat_27H_3 27 0 729 0 729 0
Salt_3H_1 0 3 9 0 0 9
Salt_3H_2 0 3 9 0 0 9
Salt_3H_3 0 3 9 0 0 9
Salt_9H_1 0 9 81 0 0 81
Salt_9H_2 0 9 81 0 0 81
Salt_9H_3 0 9 81 0 0 81
Salt_27H_1 0 27 729 0 0 729
Salt_27H_2 0 27 729 0 0 729
Salt_27H_3 0 27 729 0 0 729
$groups.vector
[1] "ColdvsControl" "HeatvsControl" "SaltvsControl" "Control"
[5] "ColdvsControl" "HeatvsControl" "SaltvsControl" "Control"
[9] "ColdvsControl" "HeatvsControl" "SaltvsControl"
$edesign
Time Replicate Control Cold Heat Salt
Control_3H_1 3 1 1 0 0 0
Control_3H_2 3 1 1 0 0 0
Control_3H_3 3 1 1 0 0 0
Control_9H_1 9 2 1 0 0 0
Control_9H_2 9 2 1 0 0 0
Control_9H_3 9 2 1 0 0 0
Control_27H_1 27 3 1 0 0 0
Control_27H_2 27 3 1 0 0 0
Control_27H_3 27 3 1 0 0 0
Cold_3H_1 3 4 0 1 0 0
Cold_3H_2 3 4 0 1 0 0
Cold_3H_3 3 4 0 1 0 0
Cold_9H_1 9 5 0 1 0 0
Cold_9H_2 9 5 0 1 0 0
Cold_9H_3 9 5 0 1 0 0
Cold_27H_1 27 6 0 1 0 0
Cold_27H_2 27 6 0 1 0 0
Cold_27H_3 27 6 0 1 0 0
Heat_3H_1 3 7 0 0 1 0
Heat_3H_2 3 7 0 0 1 0
Heat_3H_3 3 7 0 0 1 0
Heat_9H_1 9 8 0 0 1 0
Heat_9H_2 9 8 0 0 1 0
Heat_9H_3 9 8 0 0 1 0
Heat_27H_1 27 9 0 0 1 0
Heat_27H_2 27 9 0 0 1 0
Heat_27H_3 27 9 0 0 1 0
Salt_3H_1 3 10 0 0 0 1
Salt_3H_2 3 10 0 0 0 1
Salt_3H_3 3 10 0 0 0 1
Salt_9H_1 9 11 0 0 0 1
Salt_9H_2 9 11 0 0 0 1
Salt_9H_3 9 11 0 0 0 1
Salt_27H_1 27 12 0 0 0 1
Salt_27H_2 27 12 0 0 0 1
Salt_27H_3 27 12 0 0 0 1
$dis
Time TimexTissue1 TimexTissue2 TimexTissue3 TimexTissue4 Time2
Array1 0 0 0 0 0 0
Array2 0 0 0 0 0 0
Array3 2 2 0 0 0 4
Array4 2 2 0 0 0 4
Array5 2 0 0 2 0 4
Array6 2 0 0 2 0 4
Array7 2 0 0 0 0 4
Array8 2 0 0 0 0 4
Array9 2 0 2 0 0 4
Array10 2 0 2 0 0 4
Array11 2 0 0 0 2 4
Array12 2 0 0 0 2 4
Array13 4 4 0 0 0 16
Array14 4 4 0 0 0 16
Array15 4 0 0 4 0 16
Array16 4 0 0 4 0 16
Array17 4 0 0 0 0 16
Array18 4 0 0 0 0 16
Array19 4 0 4 0 0 16
Array20 4 0 4 0 0 16
Array21 4 0 0 0 4 16
Array22 4 0 0 0 4 16
Array23 6 6 0 0 0 36
Array24 6 6 0 0 0 36
Array25 6 0 0 6 0 36
Array26 6 0 0 6 0 36
Array27 6 0 0 0 0 36
Array28 6 0 0 0 0 36
Array29 6 0 6 0 0 36
Array30 6 0 6 0 0 36
Array31 6 0 0 0 6 36
Array32 6 0 0 0 6 36
Time2xTissue1 Time2xTissue2 Time2xTissue3 Time2xTissue4 Time3
Array1 0 0 0 0 0
Array2 0 0 0 0 0
Array3 4 0 0 0 8
Array4 4 0 0 0 8
Array5 0 0 4 0 8
Array6 0 0 4 0 8
Array7 0 0 0 0 8
Array8 0 0 0 0 8
Array9 0 4 0 0 8
Array10 0 4 0 0 8
Array11 0 0 0 4 8
Array12 0 0 0 4 8
Array13 16 0 0 0 64
Array14 16 0 0 0 64
Array15 0 0 16 0 64
Array16 0 0 16 0 64
Array17 0 0 0 0 64
Array18 0 0 0 0 64
Array19 0 16 0 0 64
Array20 0 16 0 0 64
Array21 0 0 0 16 64
Array22 0 0 0 16 64
Array23 36 0 0 0 216
Array24 36 0 0 0 216
Array25 0 0 36 0 216
Array26 0 0 36 0 216
Array27 0 0 0 0 216
Array28 0 0 0 0 216
Array29 0 36 0 0 216
Array30 0 36 0 0 216
Array31 0 0 0 36 216
Array32 0 0 0 36 216
Time3xTissue1 Time3xTissue2 Time3xTissue3 Time3xTissue4
Array1 0 0 0 0
Array2 0 0 0 0
Array3 8 0 0 0
Array4 8 0 0 0
Array5 0 0 8 0
Array6 0 0 8 0
Array7 0 0 0 0
Array8 0 0 0 0
Array9 0 8 0 0
Array10 0 8 0 0
Array11 0 0 0 8
Array12 0 0 0 8
Array13 64 0 0 0
Array14 64 0 0 0
Array15 0 0 64 0
Array16 0 0 64 0
Array17 0 0 0 0
Array18 0 0 0 0
Array19 0 64 0 0
Array20 0 64 0 0
Array21 0 0 0 64
Array22 0 0 0 64
Array23 216 0 0 0
Array24 216 0 0 0
Array25 0 0 216 0
Array26 0 0 216 0
Array27 0 0 0 0
Array28 0 0 0 0
Array29 0 216 0 0
Array30 0 216 0 0
Array31 0 0 0 216
Array32 0 0 0 216
$groups.vector
[1] "Control" "Tissue1vsControl" "Tissue2vsControl" "Tissue3vsControl"
[5] "Tissue4vsControl" "Control" "Tissue1vsControl" "Tissue2vsControl"
[9] "Tissue3vsControl" "Tissue4vsControl" "Control" "Tissue1vsControl"
[13] "Tissue2vsControl" "Tissue3vsControl" "Tissue4vsControl"
$edesign
Time Replicates Control Tissue1 Tissue2 Tissue3 Tissue4
Array1 0 1 1 1 1 1 1
Array2 0 1 1 1 1 1 1
Array3 2 2 0 1 0 0 0
Array4 2 2 0 1 0 0 0
Array5 2 3 0 0 0 1 0
Array6 2 3 0 0 0 1 0
Array7 2 4 1 0 0 0 0
Array8 2 4 1 0 0 0 0
Array9 2 5 0 0 1 0 0
Array10 2 5 0 0 1 0 0
Array11 2 6 0 0 0 0 1
Array12 2 6 0 0 0 0 1
Array13 4 7 0 1 0 0 0
Array14 4 7 0 1 0 0 0
Array15 4 8 0 0 0 1 0
Array16 4 8 0 0 0 1 0
Array17 4 9 1 0 0 0 0
Array18 4 9 1 0 0 0 0
Array19 4 10 0 0 1 0 0
Array20 4 10 0 0 1 0 0
Array21 4 11 0 0 0 0 1
Array22 4 11 0 0 0 0 1
Array23 6 12 0 1 0 0 0
Array24 6 12 0 1 0 0 0
Array25 6 13 0 0 0 1 0
Array26 6 13 0 0 0 1 0
Array27 6 14 1 0 0 0 0
Array28 6 14 1 0 0 0 0
Array29 6 15 0 0 1 0 0
Array30 6 15 0 0 1 0 0
Array31 6 16 0 0 0 0 1
Array32 6 16 0 0 0 0 1
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.