script/GSE74065_MEF_iGABA_reprogramming_data_processing.R

In BioHPC/LONGO: Long gene expression as a metric for neuronal identity

# Colasante et al., Cell Stem Cell 2015
# Data obtained from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74065
# File name: GSE74065_counts.table.csv.gz

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# Raw data processing information
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# GSE74065_counts.table.csv.gz was edited so that sample names were added, and only
# gene counts were saved. Output file is named GSE74065_MEF_reprogramming_iGABA_mouse.csv

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# LONGO processing information
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# Species: Mmusculus
# Gene ID: ensembl_gene_id
# Data filtered (>1 cpm for at least 4 samples)
# Quantile normalized
# Sliding median
# Multi probe values averaged
# Bin size: 200
# Step size: 40
# Control column: Sample 1