Data from the microarray experiment of human, bonobo and gorilla cultured fibroblasts done by Karaman et al. (2003)

Description

Total RNA from early-passage primary fibroblast cell lines from 18 human, 10 bonobo and 11 gorilla donors was extracted and gene-expression analysis performed using Affymetrix U95Av2.

Usage

data(fibroEset)

Format

Expression set with 12625 genes and 46 samples.
There are 2 covariates listed.

• samp: sample code.

• species: The species the sample was obtained from.
  h: human (Homo sapiens), b: bonobo (Pan paniscus), g: gorilla (Gorilla gorilla)

Details

Data preprocessing (as described in the publication):
The raw expression scores for every gene in every sample were generated using AFFYMETRIX GENECHIP 5.0. Normalization was done by calculating multiplicative scaling factors on the basis of the median intensity of the 60th to 95th percentile of gene-expression scores. All gene-expression scores below 100 were set to 100 to minimize noise associated with less robust measurements of rare transcripts.

The usage of a human chip can cause mismatches between the ape RNA samples and human oligonucleotide probes. Because 16 perfect match probes interrogate each gene, the effect of mismatches should be minimal (Hacia et al. 1998).

Source

http://lichad.usc.edu/supplement/index.html

References

Karaman M.W., Houck M.L., Chemnick L.G., Nagpal S., Chawannakul D., Sudano D., Pike B.L., Ho V.V., Ryder O.A. & Hacia J.G. (2003) Comparative Analysis of Gene-Expression Patterns in Human and African Great Ape Cultured Fibroblasts. Genome Research 13, 1619-1630.

Hacia J.G. et al. (1998) Evolutionary sequence comparisons using high-density oligonucleotide arrays. Nature genetics 18, 155-158.

Examples

library(Biobase)
data(fibroEset)
xx <- exprs(fibroEset)
colnames(xx) <- as.character(fibroEset$species)
dim(xx)
xx[1:5,1:5]
fibroEset$species
featureNames(fibroEset)[1:20]

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(fibroEset)
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/fibroEset/fibroEset.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fibroEset
> ### Title: Data from the microarray experiment of human, bonobo and gorilla
> ###   cultured fibroblasts done by Karaman et al. (2003)
> ### Aliases: fibroEset
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(Biobase)
> data(fibroEset)
> xx <- exprs(fibroEset)
> colnames(xx) <- as.character(fibroEset$species)
> dim(xx)
[1] 12625    46
> xx[1:5,1:5]
             b   b   b    b   b
100_g_at   476 518 686  602 470
1000_at   1795 890 508 1113 708
1001_at    100 119 100  100 100
1002_f_at  100 101 100  100 100
1003_s_at  100 100 100  100 100
> fibroEset$species
 [1] b b b b b b b b b b b g g g g g g g g g g g g h h h h h h h h h h h h h h h
[39] h h h h h h h h
Levels: b g h
> featureNames(fibroEset)[1:20]
 [1] "100_g_at"  "1000_at"   "1001_at"   "1002_f_at" "1003_s_at" "1004_at"  
 [7] "1005_at"   "1006_at"   "1007_s_at" "1008_f_at" "1009_at"   "101_at"   
[13] "1010_at"   "1011_s_at" "1012_at"   "1013_at"   "1014_at"   "1015_s_at"
[19] "1016_s_at" "1017_at"  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>