Reproducibility between Fresh and Frozen B-cell subtypes

Description

This dataset contains a data.frame of t-scores (from a Linear mixed effects model) and p-values for differential expression between pre (Im, N) and post germinal (M, PB) centre cells within peripheral blood. The first and second column contain the the test for the hypothesis of no differentially expression between pre and post germinal cells for the freshly sorted and gene profiled cells. The third and fourth column contain the the test for the hypothesis of no differentially expression between pre and post germinal cells for the cryopreserved (frozen), thawed, sorted, and gene profiled cells. The fifth and sixth column contain the the test for the hypothesis of no differentially expression between fresh and frozen cells. The used array type was Affymetrix Human Exon 1.0 ST microarray.

Format

The format of the data.frame is:

'data.frame': 18708 obs. of 6 variables:
$ PreVsPost.Fresh.tstat : num -1.073 -0.381 -1.105 -0.559 -1.054 ...
$ PreVsPost.Fresh.pval : num 0.283 0.703 0.269 0.576 0.292 ...
$ PreVsPost.Frozen.tstat: num -0.245 -0.731 -0.828 -0.568 -1.083 ...
$ PreVsPost.Frozen.pval : num 0.806 0.465 0.408 0.57 0.279 ...
$ FreshVsFrozen.tstat : num 0.836 1.135 -0.221 0.191 -0.783 ...
$ FreshVsFrozen.pval : num 0.403 0.256 0.825 0.849 0.434 ...

Details

Further details can be found in Rasmussen and Bilgrau et al. (2015).

Author(s)

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

References

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(freshVsFrozen)
str(freshVsFrozen)

# Plot P-values
plot(freshVsFrozen[,c(2,4)], cex = 0.5)

# Plot ranked and scaled P-values
plot(Uhat(abs(freshVsFrozen[,c(1,3)])), 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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(GMCM)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GMCM/freshVsFrozen.Rd_%03d_medium.png", width=480, height=480)
> ### Name: freshVsFrozen
> ### Title: Reproducibility between Fresh and Frozen B-cell subtypes
> ### Aliases: freshVsFrozen
> ### Keywords: data datasets,
> 
> ### ** Examples
> 
> data(freshVsFrozen)
> str(freshVsFrozen)
'data.frame':	18708 obs. of  6 variables:
 $ PreVsPost.Fresh.tstat : num  -1.073 -0.381 -1.105 -0.559 -1.054 ...
 $ PreVsPost.Fresh.pval  : num  0.283 0.703 0.269 0.576 0.292 ...
 $ PreVsPost.Frozen.tstat: num  -0.245 -0.731 -0.828 -0.568 -1.083 ...
 $ PreVsPost.Frozen.pval : num  0.806 0.465 0.408 0.57 0.279 ...
 $ FreshVsFrozen.tstat   : num  0.836 1.135 -0.221 0.191 -0.783 ...
 $ FreshVsFrozen.pval    : num  0.403 0.256 0.825 0.849 0.434 ...
> 
> # Plot P-values
> plot(freshVsFrozen[,c(2,4)], cex = 0.5)
> 
> # Plot ranked and scaled P-values
> plot(Uhat(abs(freshVsFrozen[,c(1,3)])), cex = 0.5)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>