PAH and PCBs

[SaidSalehe]

I have created this thread for posting and getting comments on our PCB -Pulmonary Arteriole Hypertension (PAH) project.

Several studies including the Flemish Adults Study have shown that exposure to Chemicals like Polychlorinated Biphenyl (PCBs) is associated with changes in gene expression. In this study we hypothesize that genes associated with PAH are differently expressed by sex and levels of exposure to PCB's. By using microarray data and internal exposure levels of PCBs from the Flemish Adult Study (deposited in GEO), We aim to determine whether PAH-associated genes are differently expressed among individuals exposed to low and high PCBs levels, determine whether there is sex difference in PAH gene expression among individuals exposed to high levels of PCBs, and conduct gene enrichment analysis to identify causal pathways contributing to hyper-proliferative vascular lessons.

As a first step to this project, I have been working on obtaining data from the GEO website. I followed the steps for Microarray data cleaning posted in the forum by "Stemoore" in February 20, 2018 and its update of March 13, 2018.

Data source: From the GEO website, I downloaded the Series Matrix File(s) [GSE44422_series_matrix.txt.gz], Platform [GPL6480] and another additional file named [Annotation Soft Table] - though I wasn't sure how this annotation table was used in the code.

I then run the "RCleanDscret.R" as per instruction posted in the Forum. I got more more or less the same results as many did except that I have five output files instead of four as suggested. My output files are attached below.