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Using R to read a GSE table

I downloaded supplementary files by running this command in R,

filePaths = getGEOSuppFiles("GSE60341")

This created two files,

  1. GSE60341_nanostring_processed_data.txt; and

  2. GSE60341_RAW

How can I make R read GSE60341_nanostring_processed_data.txt as a meaningful data frame?

Solution

  • read.table is probably the best option and will even read in a *.gz file:

    temp <- read.table("GSE60341/GSE60341_nanostring_processed_data.txt.gz")
> dim(temp)
[1]  251 1950

    There is a great GEOquery tutorial here