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Comparing GO terms with R Bioconductor

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Help with Gene Ontology (GO) using R Bioconductor for yeast microarray analysis for visually impaired student needed

I am a visually impaired bioinformatics graduate student using microarray data for my master’s thesis aimed at deciphering the mechanism by which the yeast wild type can suppress the rise of free reactive oxygen species (ROS) induced by caloric restriction (CR) thus extending lifespan but the Atg15 and Erg6 knockout mutant cannot.  

Since my remaining vision is very limited I need very high magnification.  But that makes my visual field very small.  Therefore I need somebody to teach me how to use these programming environments, especially for microarray analysis, next generation sequencing and constructing gene and pathway interaction networks.  This is very difficult for me to figure out without assistance because Zoomtext, my magnification and text to speech software, on which I am depending because I am almost blind, has problems reading out aloud many programming related websites to me.  

Since I am legally blind the rehab agency is giving me money to pay tutors.  I need urgent help because if I cannot turn in my thesis within the next month my funding will be discontinued. The training can be done remotely using TeamViewer 5 and Skype.  Using Team Viewer 5 is free.  Team Viewer 5 can be downloaded at http://www.teamviewer.com/en/download/dyngate.aspx#version5 

To complete my thesis, I need to compare GO (Gene Ontology) terms.  The GO terms can be retrieved from the following website: http://amigo.geneontology.org/amigo.  If you know how to use this website please contact me.  Good knowledge of the statistical software R is required.

I also need help in implementing the following instructions into my R script: 

try
http://www.broadinstitute.org/gsea/msigdb/collections.jsp#C5 there you
can download the whole list of gene ontologies as .gmt file. You can
read this file in with getGMT() from the gseabase bioconductor package.
this will return you a list, with names equal to gene set names, and
associated element a vector of genes.  

If you can teach this to me please contact me quickly because I need to have completed this task in less than a week in order to remain eligible for funding.  

I have copy-pasted the latest version of the R code I am currently using in attached document. Although this code is long, please look at the very end of this attached document after the R code finishes because you will find the most important information there.  

Please also contact me if you are familiar with yeast biology because I am using Affymetrix microarray data from saccharomyces cerevisiae.  I need help in searching the literature to find out what other researchers have published about the genes and pathways that were identified as significantly differentially expressed in our dataset.  


I am very much looking forward to share more details with you.  I thank you very much in advance for considering assisting me in earning a PhD in bioinformatics despite being almost blind.  I am grateful for your thoughts, ideas, suggestions, recommendations, advice, assistance, time, help, efforts and support.

With very warm regards, 

Thomas Hahn ... Show more
Tom S United States