Murine Secondary Palate Development miRNA Expression Data

Description

This data set contains two-color miRNA microarray expression data obtained from mouse embryonic tissue during gestational days (GD) 12, 13, and 14, which represents the critical period of palate development in the mouse.

Usage

data(PalateData)

Format

The data are in the format of an "RGList", which in this case is a list with the following 9 elements:

R

matrix of dimension 6336 x 9 which contains the red channel foreground measurements

G

matrix of dimension 6336 x 9 which contains the green channel foreground measurements

Rb

matrix of dimension 6336 x 9 which contains the red channel background measurements

Gb

matrix of dimension 6336 x 9 which contains the green channel background measurements

source

source of the images, here "imagene"

Field.Dimensions

numeric vector giving the field dimensions of the array (Metarows, Metacols, Rows and Cols)

weights

matrix of dimension 6336 x 9 which contains the quality weights associated with each spot on the arrays

printer

list containing information on the process used to print the spots on the arrays (number of grid rows / columns and number of spot rows / columns per grid - coincides with Field.Dimensions)

genes

A data.frame containing information on each probe. Has the following columns:

Field

field position for the probe

Meta Row

meta row position for the probe

Meta Column

meta column position for the probe

Row

row position for the probe

Column

column position for the probe

Gene ID

unique gene identifier provided by Miltenyi Biotec

ID

unique probe identifier constructed by concatentating the "Gene ID" with "Meta Row", "Meta Column", "Row", and "Column" information

Name

name of the microRNA

Name.stem

base name of the microRNA

probe.type

type of probe, "MMU miRNAs", "Other miRNAs", "Control", "Empty", and "Other"

Details

RNA samples were isolated from mouse embryonic orofacial tissues (GD-12 - GD-14) and fluorescently labeled with Hy5 (red). Control samples (miRXplore Universal Reference) were labeled with Hy3 (green). The two sets of samples were hybridized to miRXplore Microarrays (Miltenyi Biotec) sing the a-Hyb Hybridization Station (Miltenyi Biotec). Probes for a total of 1336 mature miRNAs (from human, mouse, rat and virus), including positive control and calibration probes, were spotted in quadruplicate on each microarray. Each array included probes for 588 murine miRNAs.

Source

P. Mukhopadhyay, G. Brock, V. Pihur, C. Webb, M.M. Pisano, and R.M. Greene. Developmental microRNA expression profiling of murine embryonic orofacial tissue. Birth Defects Res A Clin Mol Teratol, 88(7):511-34, 2010.

Examples

data(PalateData)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MmPalateMiRNA)
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: xtable
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: statmod
Loading required package: lattice
Loading required package: vsn
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MmPalateMiRNA/PalateData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: PalateData
> ### Title: Murine Secondary Palate Development miRNA Expression Data
> ### Aliases: PalateData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(PalateData)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>