GerkeLab / GSE46691

Download and import GSE46691 into R with updated HUGO gene names

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Downloads and loads GSE46691.

There are various checkpoints built into the script as several steps are computationally or memory intensive. Note that you will likely need more than 16GB of RAM for these scripts to run comfortably.

Probeset Annotations

For this script to work, visit http://www.affymetrix.com/support/technical/byproduct.affx?product=huexon-st and download HuEx-1_0-st-v2.na36.hg19.probeset.csv.zip. Save the zip file in the data folder and extract.

HUGO Dictionary

The HUGO Gene Name dictionary includes the most recent HUGO gene names list. See https://beta.genenames.org/download/custom/ for more information.

To update the HUGO gene list, delete data/hgnc_dict.tsv and the file will be re-downloaded on the next run.

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Download and import GSE46691 into R with updated HUGO gene names


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Language:R 100.0%