How to extract expression data from RAW data.
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4.6 years ago
hkarakurt ▴ 130

Hello. I downloaded GSE57821 RAW data by getGEOSuppFiles command in R and now I have "filelist.txt" and GSE57821_RAW.tar files.

My command: gse <- getGEO("GSE57821", GSEMatrix = TRUE)

raw <- getGEOSuppFiles("GSE57821")

I want to normalize RAW data. Which way should I follow? How can I retrieve expression data from raw data?

exprs command is not working both in gse and raw files.

I am relatively new at gene expression analysis in R.

Thank you.

raw expression • 3.6k views
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Entering edit mode
4.6 years ago
h.mon 33k

The "raw" data is, in fact, a tar file containing several compressed tables of counts. Maybe someone knows a function which directly reads the "raw" file and creates a ExpressionSet or DGEList - I don't. But getGEOSuppFiles() does not either:

No parsing of the downloaded files is attempted, since the file format is not generally knowable by the computer.

You have to untar GSE57821_RAW.tar and then uncompress the counts files, read one by one with read.table() and finally create the ExpressionSet or DGElist objects yourself.