fdata: Example of dataset for the fcros package.

In fcros: A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

Description

This is a synthetic dataset generated using the "madsim" R package (available from the CRAN web site). Two biological conditions data matrix using 10,000 genes and 20 samples (10 control and 10 test samples) were simulated. 108 and 102 genes of this dataset are down- and up-regulated, respectively.

Usage

data(fdata)

Format

A data frame with 10,000 observations on the following 22 variables.

index:

a text for the genes, unique ID

cont01:

a numeric vector with log2 intensities for control sample 01

cont02:

a numeric vector with log2 intensities for control sample 02

cont03:

a numeric vector with log2 intensities for control sample 03

cont04:

a numeric vector with log2 intensities for control sample 04

cont05:

a numeric vector with log2 intensities for control sample 05

cont06:

a numeric vector with log2 intensities for control sample 06

cont07:

a numeric vector with log2 intensities for control sample 07

cont08:

a numeric vector with log2 intensities for control sample 08

cont09:

a numeric vector with log2 intensities for control sample 09

cont10:

a numeric vector with log2 intensities for control sample 10

test01:

a numeric vector with log2 intensities for test sample 01

test02:

a numeric vector with log2 intensities for test sample 02

test03:

a numeric vector with log2 intensities for test sample 03

test04:

a numeric vector with log2 intensities for test sample 04

test05:

a numeric vector with log2 intensities for test sample 05

test06:

a numeric vector with log2 intensities for test sample 06

test07:

a numeric vector with log2 intensities for test sample 07

test08:

a numeric vector with log2 intensities for test sample 08

test09:

a numeric vector with log2 intensities for test sample 09

test10:

a numeric vector with log2 intensities for test sample 10

DE_status:

a numeric vector with values -1, 0 and 1. Value 0 is used for no change genes, while -1 and 1 are used for down- and up-regulated genes, respectively.

Details

This dataset is obtained using the microarray data simulation model implemented in the package "madsim". A real microarray data, "madsim_test", was used as seed and the number of the control and the test samples were set to 10. The parameter "sdn" was set to 0.3 and all the other parameters in the madsim package were set to their default settings.

References

Dembele D, A flexible microarray data simulation model. Microarrays, 2013, v.2, n.2, pp.115-130

Examples

   data(fdata)

   rownames(fdata) <- fdata[,1];

   op <- par(mfrow = c(2,1));

   #  perform MA plot using samples "cont01" and "cont05"
   A1 <- 0.5*(fdata$cont01 + fdata$cont05);
   M1 <- fdata$cont05 - fdata$cont01;

   plot(A1, M1, col="red", xlim=c(2,18), ylim=c(-5,5),
            main="MA plot with two control samples");
   lines(x = c(2,18), y = c(0,0), col = "blue")
   lines(x = c(2,18), y = c(-1,-1), col = "blue")
   lines(x = c(2,18), y = c(1,1), col = "blue")

   #  perform MA plot using samples "cont01" and "test05"
   A2 <- 0.5*(fdata$cont01 + fdata$test05);
   M2 <- fdata$test05 - fdata$cont01;

   plot(A2, M2, col="red", xlim=c(2,18), ylim=c(-5,5),
            main="MA plot with one control and one test samples");
   lines(x = c(2,18), y = c(0,0), col = "blue")
   lines(x = c(2,18), y = c(-1,-1), col = "blue")
   lines(x = c(2,18), y = c(1,1), col = "blue")
   par(op)

Example output

fcros documentation built on May 31, 2019, 5:03 p.m.