Final Project
Condições de conclusão
Aberto: segunda-feira, 19 nov. 2018, 00:00
Vencimento: quinta-feira, 10 dez. 2020, 22:55
Dear class.
Your final project should be clear by now. Each of you has a GSE data, which I manually checked with each of you.
An overview of your data can be fin using the following link:
http://www.ncbi.nlm.nih.gov/sites/GDSbrowser/
You should also know how to download your data.
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library(Biobase)
library(GEOquery)
library(limma)
# load series and platform data from GEO
gset <- getGEO("GSEXXXXX", GSEMatrix =TRUE) ##downloads your study
gset <- gset[[1]] #extract the first element in the list
dat <- exprs(dat) #extract the expression data into a data matrix
dat.anno <- pData(dat) #extract the annotation data into a data frame.
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From there, you should have your annotation file and your gene expression data. Each of you will be working with different data sets and different platforms (cDNA arrays, Affy arrays, dual channel, single channel, etc.). You can find the platform that is specific to your study by looking for the GPLXXXX in your GSE page.
For the final project. You will submit only ONE (1) file. The file should be a Rmarkdown file. As I explained yesterday, you can create a Rmarkdown by visiting your Rstudio page, and File > New File > R Markdown. It may ask you to upgrade, say yes or ok. Enter your title and your name and select 'HTML'. When it is complete, it will create a R markdown template file. (You can see some lessons here)
You will use this to generate your final project which should contain the following:
- Introduction about the project, the platform, the samples. You should have a min of 500 words.
- Objective
- Process, analyze (supervised/unsupervised) and interpret the results.
You have all the necessary instructions as provided to you throughout the course, so there should be no confusion. I will be looking for complete projects, with clear description for each command and plots. Each step in your analysis should contain reasons and interpretations of the results.
Again, you will only send me a Rmarkdown file. I will not accept a PDF, HTML, PPT, doc, etc. If you do not send me a Rmarkdown file with the interpretation and steps clearly outlined, you will receive a zero.
You have till Dec 8, 20146 at 14 hours to submit your final project. If you have any questions, doubts or concerns, please send an e-mail.
Also, we will no longer have any classes, giving ample time to complete the assignment.
Good luck and thanks.