u133VsExon: Reproducibility between U133 plus 2 and Exon microarrays

In GMCM: Fast Estimation of Gaussian Mixture Copula Models

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 <[e-mail]>

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)

Example output

'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 ...

GMCM documentation built on Nov. 6, 2019, 1:08 a.m.