GSE19138 Processing Pipeline

Publication

Nature structural & molecular biology (2010) — PMID 20062054

Dataset

Comprehensive discovery of endogenous Argonaute binding sites in C. elegans

1. 1

   C. elegans GeneChip arrays were analyzed by using affymetrix power tools (command line arguments apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d Celegans.CDF)

   Microarray vNot specified

   $ Bash example

   # Install Affymetrix Power Tools (APT) if not already installed.
   # APT is proprietary software from Thermo Fisher Scientific (formerly Affymetrix).
   # Installation typically involves downloading from their official website and following their instructions.
   # For example, on Linux, it might involve a package manager or direct download and installation.
   # There isn't a simple 'conda install affymetrix-power-tools' command that works for the full suite.
   # Ensure the Celegans.CDF file is available in the current directory or specified path.
   # This file defines the probe sets for the C. elegans GeneChip array and is typically obtained from Affymetrix/Thermo Fisher Scientific.
   
   # Run apt-probeset-summarize with RMA-sketch and PLIER-MM-sketch algorithms
   apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d Celegans.CDF

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Tools Used