Reproducibility between U133 plus 2 and Exon microarrays

Description

This dataset contains a data.frame of unadjusted P-values for differential expression between germinal center cells and other B-cells within tonsils for two different experiments. The experiments differ primarily in the microarray platform used. The first column corresponds the evidence from the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. The second column corresponds to the Affymetrix GeneChip Human Exon 1.0 ST Array.

Format

The format of the data.frame is:

'data.frame': 19577 obs. of 2 variables:
$ u133: num 0.17561 0.00178 0.005371 0.000669 0.655261 ...
$ exon: num 1.07e-01 6.74e-10 1.51e-03 6.76e-05 3.36e-01 ...

Details

Further details can be found in Bergkvist et al. (2014) and Rasmussen and Bilgrau et al. (2014).

Author(s)

Anders Ellern Bilgrau <anders.ellern.bilgrau@gmail.com>

References

Bergkvist, Kim Steve, Mette Nyegaard, Martin Boegsted, Alexander Schmitz, Julie Stoeve Boedker, Simon Mylius Rasmussen, Martin Perez-Andres et al. (2014). "Validation and Implementation of a Method for Microarray Gene Expression Profiling of Minor B-Cell Subpopulations in Man". BMC immunology, 15(1), 3.

Rasmussen SM, Bilgrau AE, Schmitz A, Falgreen S, Bergkvist KS, Tramm AM, Baech J, Jacobsen CL, Gaihede M, Kjeldsen MK, Boedker JS, Dybkaer K, Boegsted M, Johnsen HE (2015). "Stable Phenotype Of B-Cell Subsets Following Cryopreservation and Thawing of Normal Human Lymphocytes Stored in a Tissue Biobank." Cytometry Part B: Clinical Cytometry, 88(1), 40-49.

Examples

data(u133VsExon)
str(u133VsExon)

# Plot P-values
plot(u133VsExon, cex = 0.5)

# Plot ranked and scaled P-values
plot(Uhat(1-u133VsExon), cex = 0.5)

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(GMCM)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GMCM/u133VsExon.Rd_%03d_medium.png", width=480, height=480)
> ### Name: u133VsExon
> ### Title: Reproducibility between U133 plus 2 and Exon microarrays
> ### Aliases: u133VsExon
> ### Keywords: data datasets,
> 
> ### ** Examples
> 
> data(u133VsExon)
> str(u133VsExon)
'data.frame':	19577 obs. of  2 variables:
 $ u133: num  0.17561 0.00178 0.005371 0.000669 0.655261 ...
 $ exon: num  1.07e-01 6.74e-10 1.51e-03 6.76e-05 3.36e-01 ...
> 
> # Plot P-values
> plot(u133VsExon, cex = 0.5)
> 
> # Plot ranked and scaled P-values
> plot(Uhat(1-u133VsExon), cex = 0.5)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>