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- | **2016 REU program**\\ | ||
- | | + | |
+ | **An R test** \\ | ||
+ | This simple question is designed to test the applicants on their expertise in R, self learning, working under pressure, presenting their results, and explaining their work.\\ | ||
+ | - Install [[https:// | ||
- Have a look at the [[https:// | - Have a look at the [[https:// | ||
- Install [[http:// | - Install [[http:// | ||
- Write a script that downloads GSE59259 dataset and computes the list of differentially expressed genes with adjusted p-value better than 0.01. The first lines of your script look like these: | - Write a script that downloads GSE59259 dataset and computes the list of differentially expressed genes with adjusted p-value better than 0.01. The first lines of your script look like these: | ||
- library(limma) | - library(limma) | ||
- | | + | |
- | gset <- getGEO(" | + | library(GEOquery) |
- | type <- c(rep(" | + | |
- | des <- ???? | + | < |
- | Data <- log(exprs(gset[[1]])+0.001) | + | |
- | fit <- ImFit(Data, des) ## ! | + | type <- c(rep(" |
- | ... | + | des <- ???? |
- | - The rest of the script follows the instruction in Section 3.2 (Sample limma Session) with appropriate modifications. | + | Data <- log(exprs(gset[[1|]])+0.001) |
- | - Your script should save the list of differentially expressed (DE) genes and in csv format in a file named " | + | fit <- ImFit(Data, des) ## ! |
- | - Use pheatmap function to plot the expression of the top 5 DE genes. | + | ... |
- | - **Deliverables**: | + | - The rest of the script follows the instruction in Section 3.2 (Sample limma Session) with appropriate modifications. |
- | - You need to be able to orally explain all parts of your script including the above lines. Be prepared to explain the input, output, and process done by each function you use. | + | - Your script should save the list of differentially expressed (DE) genes and in csv format in a file named " |
- | - If you are not familiar with gene expression and have little idea what limma does, try to learn the needed concept from the web, e.g., [[https:// | + | - Use pheatmap function to plot the expression of the top 5 DE genes. |
+ | - **Deliverables**: | ||
+ | - You need to be able to orally explain all parts of your script including the above lines. Be prepared to explain the input, output, and process done by each function you use. | ||
+ | - If you are not familiar with gene expression and have little idea what limma does, try to learn the needed concept from the web, e.g., [[https:// | ||
+ | </ | ||
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