fdata {fcros} | R Documentation

## Example of dataset for the fcros package.

### 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)

[Package fcros version 1.6.1 Index]