Question about gene length used in CQN normaliztion

Hi , Does anyone know how did the gene length and GC content have been got as input information of CQN normalization in the DE analysis of syn14237651(https://www.synapse.org/#!Synapse:syn14237651) ? Bests

Created by Min Tang boymin2020
Hi @th_vairam, Thanks for your reply. Could you tell me why you did not use the R package of EDSeq to get the gene length and GC % content? Bests,
Hi @boymin2020 We queried biomart dec 2016 archive for gene length and GC content information and used CQN package from bioconductor to account for them. Here is an example code for ROSMAP data https://github.com/Sage-Bionetworks/ampad-DiffExp/blob/master/gene_level_analysis/ROSMAP_geneLevel.Rmd

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Hi , Does anyone know how did the gene length and GC content have been got as input information of CQN normalization in the DE analysis of syn14237651(https://www.synapse.org/#!Synapse:syn14237651) ? Bests

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