Dissecting Inflammatory Complications in Critically Injured Patients by Within-Patient Gene Expression Changes: A Longitudinal Clinical Genomics Study - Supplemental Data



 

Desai KH*, Tan CS*, Leek JT, Maier RV, Tompkins RG, Storey JD#

PLoS Med 8(9): e1001093. doi:10.1371/journal.pmed.1001093

PubMed ID:21931541

*These authors contributed equally to this work.
#Corresponding author, jstorey@princeton.edu.

Instructions for downloading computer code plus data to reproduce the analyses:

Step 1. Download and Install R from http://cran.r-project.org/. (R is a free and popular statistical software package. We utilized R to perform all data analyses. We strongly recommend using all default settings in the installation process.)

Step 2.Create a local folder called Trauma.

Step 3. Download the following *.zip file to the local folder Trauma:

Unzip this file by double-clicking on it, which will yield a folder called DatasetS1_withdata. This folder contains our R scripts PLUS normalized microarray data, clinical data, and other supporting data needed to perform the entire analysis. Instructions for how to run our R code are provided in Step 6.

(NOTE: Steps 4 and 5 are optional. If you do not plan to normalize the microarray data by yourself, then you may skip Steps 4 and 5.)

Step 4. Download the dChip WINDOWS normalization software package from https://sites.google.com/site/dchipsoft/downloading-dchip-software (we used dchip_2010_01.exe). Rename this file to dchip.exe (drop the version info) and copy this *.exe to the local folder Trauma/Dataset S1_withdata/data/CEL/. (NOTE: The downloaded dChip software runs only on Windows platform so you will need access to a Windows machine to carry out the option Steps 4 and 5.)

Step 5. Download these eight *.zip files to the local folder Trauma:

Unzip cel1.zip by double-clicking on it. This will yield a folder called CEL1. Move all the *.CEL files from the folder CEL1 to the local folder Trauma/DatasetS1_withdata/data/CEL/. Repeat the same process for cel2.zip, cel3.zip, …, cel8.zip. These eight *.zip files contain in total 797 *.CEL files. Each *.zip file is around 0.8GB, where cel1.zip to cel7.zip contain 100 *.CEL files each, and cel8.zip contains 97 *.CEL files.

Step 6. To reproduce the analyses, go to Trauma/DatasetS1_withdata/ and double-click on the file runAnalysis.Rdata and the R Console will be launched. If no text appears on the R Console, type the following in the R Console after the symbol ">":
start.analysis()
Once the above string is typed into the R console, hit the enter button. The scripts should start running now and follow the instructions printed out in the R Console.

For further information concerning our analysis workflow see:
a. Trauma/DatasetS1_withdata/README.rtf: This file contains basic information for our entire analysis workflow.
b. Trauma/DatasetS1_withdata/documentation/Information.rtf: This file contains information on the structure of Trauma/Dataset S1/ and how to run our R code in a quick and simple way.
c. Text S2, the supplementary text of the PLoS Medicine paper for details on the algorithms and the workflow.