So in our Multi-dimensional Modeling and Reconstruction of Signaling Networks in Salmonella-infected Human Cells project, we have several methods to construct the networks so the data is still needed to be preprocessed so that it can be ready to be analyzed with these methods. One method needed to have a matrix first row as protein name and time series (2 min, 5 min, 10 min, 20 min), and the values of the proteins in each time series were to be 1 or 0 according to variance, significance and the size of fold change.

Since we’ll be using R for most of the analyses, we converted XLS data file to CSV using MS Office Excel 2013 and then we had to fix several lines using Sublime Text 2 because three colums in these lines were left unquoted which later created a problem reading in RStudio. The data contains phosphorylation data of 8553 peptides. There are many missing data points for many peptides and since IPI IDs were used for peptides and these are not supported now, we had to convert IPI IDs to HGNC approved symbols although data had these symbols as names but they looked outdated.

In this study, we’re going to use a phosphorylation data from a research paper on phosphoproteomic analysis of related cells. The idea is to use and compare existing methods and develop these methods to be able to better understand the nature of signaling events in these cells and to find key proteins that might be targets for disease diagnosis, prevention and treatment. This study will be submitted as a research paper so I’m not going to publish any results here for now but I’ll mention the struggles I have and solutions I try to solve them.