unifiedWMWqPCR (version 1.8.0)

NBdata: Documentation for the dataset NBdata

Description

The example data used in this package, are a subset of the data provided by Mestdagh et al. (2009). The subset contains quantification cycles of 323 microRNAs in 61 neuroblastoma (NB) tumor samples: 22 MYCN amplified (called MNA) and 39 MYCN single copy samples (called MNSC). The subset was selected so that all microRNAs with a least 85 undetermined values in both groups were removed, see De Neve et al. (2013) for details.

Details

The data exists in different formats. NBdata gives you a data frame with following variables:

subject:

variable of class "factor", indicating the subject code.

miRNA:

variable of class "factor", indicating the miRNA code.

Cq:

variable of class "numeric", containing the cycle information.

group:

variable of class "factor", indicating the group code.

The data matrix NBmat contains the same data in matrix format, where the rows are the different miRNA's and the columns the different subjects. The vector NBgroups specifies to which group every column of NBmat belongs.

References

Mestdagh, P., P. Van Vlierberghe, A. De Weer, D. Muth, F. Westermann, F. Speleman, and J. Vandesompele (2009) A novel and universal method for microRNA RT-qPCR data normalization. Genome Biology., 10, R64.

De Neve, J. Thas, O. Ottoy, J.P. and Clement L. (2013) An extension of the Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data. Statistical Applications in Genetics and Molecular Biology. 12, 333-346.

Examples

# Look at the data frame
data(NBdata)
str(NBdata)

# Look at the matrix and grouping vector
data(NBmat)
str(NBmat)
str(NBgroups)