I’m new the gene expression analysis. My data series contains expression for each probe for each given sample. I have the GPL (platform) and series number. But don’t know how to get to the gene expression for each given gene from the expression for each given probe. This should be a rather simple task for anyone in this field. But my work is stuck in this basic level. Could anyone help me with it?
The series ID is GSE65106 and the platform ID is GPL6244.
I would truly appreciate it if someone could help me with this task.
Thank you in advance.
I started doing this task based on an online course.
it used this code:
setRepositories()#install.packages(c("GEOquery", "limma", "pheatmap", "ggplot2", "gplots", "reshape2", "plyr", "pheatmap", "umap"))
setwd("D:/Study/ProbeToExpression/")
library(Biobase)library(GEOquery)library(limma)library(umap)library(pheatmap)
series <- "GSE65106"platform <- "GPL6244"
gset <- getGEO(series, GSEMatrix = TRUE, AnnotGPL=TRUE, destdir = "Data/")if (length(gset) > 1) idx <- grep(platform, attr(gset, "names")) else idx <- 1gset <- gset[[idx]]gsetclass(gset)#gset = gset[[1]]gr <- c(rep("ASD", 6), rep("CTRL", 6), rep("CTRL", 4), rep("CTRL", 4), rep("ASD", 5), rep("CTRL", 5), rep("CTRL", 3), rep("ASD", 5), rep("CTRL", 5), rep("CTRL", 3), rep("ASD", 5), rep("CTRL", 5), rep("CTRL", 3))#length(gr)
ex <- exprs(gset)write.csv(ex, file = "Results/expression_data.csv")
While based on the given instructions I expected the output CSV file to contain expression data for the genes, the rows, their headers and the number of rows were exactly the same as the series matrix.
I don’t know what went wrong. Is this code for something else?
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