Description Usage Arguments Details Value Author(s) References See Also Examples

R-I plots consist in plotting the intensity log2-ratio (R) against mean log10 intensity (I) of spot's volume data from 2D Gel experiments.

1 |

`data` |
either a dataframe or a matrix of 2D Gel Volume data. |

`n1` |
an integer. Number of replicates in condition 1. |

`n2` |
an integer. Number of replicates in condition 2. |

`...` |
Further arguments to be passed to methods, such as graphical parameters (see |

Dudoit et al (2002) proposed a method for visualization of artifacts in microarray datasets, called the MA-plot, which was transposed for proteomics data as the Ratio-Intensity plot by Meunier et al (2005). R-I plots allow to directly visualize artifacts in the original data set as well as the effects of normalization. The log2-ratio (R) is the log2 of the mean of volume data in condition 2 upon the mean of volume data in condition 1:

*
R = log2(mean(V_{Cond2})/mean(V_{Cond1}))*

The intensity (I) is the log10 of the mean of volume data in condition 2 by the mean of volume data in condition 1

*
I = log10(mean(V_{Cond2}) x mean(V_{Cond1}))*

Display the RI-plot of data, the values on the plot are the number of spots with a Ratio greater then 1 (upper values) or lesser then -1 (lower value). A list is invinsibly returns with components :

`RI` |
a dataframe with ratio and intensity values calculated. |

`diff` |
a vector with number of spots with a Ratio greater then 1 or lesser then -1 (in that order). |

Sebastien Artigaud sebastien.artigaud@gmx.com

Artigaud, S., Gauthier, O. & Pichereau, V. (2013) "Identifying differentially expressed proteins in two-dimensional electrophoresis experiments: inputs from transcriptomics statistical tools." Bioinformatics, vol.29 (21): 2729-2734.

Dudoit, S., Yang, Y.H., Callow, M.J., & Speed, T.P. (2002) "Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments" Statistica Sinica, vol. 12: 111-139.

Meunier, B., Bouley, J., Piec, I., Bernard, C., Picard, B., & Hocquette, J.-F. (2005) "Data analysis methods for detection of differential protein expression in two-dimensional gel electrophoresis" Analytical Biochemistry, vol. 340 (2): 226-230.

1 2 3 |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.