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TCGA data processing

CC Caroline Contat
PA Pierre-Benoit Ancey
NZ Nadine Zangger
SS Silvia Sabatino
JP Justine Pascual
SE Stéphane Escrig
LJ Louise Jensen
CG Christine Goepfert
BL Bernard Lanz
ML Mario Lepore
RG Rolf Gruetter
AR Anouk Rossier
SB Sabina Berezowska
CN Christina Neppl
IZ Inti Zlobec
SC Stéphanie Clerc-Rosset
GK Graham William Knott
JR Jeffrey C Rathmell
EA E Dale Abel
AM Anders Meibom
EM Etienne Meylan
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The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma (LUAD) dataset was retrieved from http://cancergenome.nih.gov. Samples with clinical information and mRNA (RNASEQV2) expression data were selected (511 samples including 448 samples with survival data), and the data were downloaded using the RTCGAtoolbox (v2.12.1). RSEM gene quantifications as provided by TCGA were taken, counts were converted to log2 normalized counts expression and batch effect was removed using voom and removeBatchEffect functions from the limma package (v3.38.3).

Copyright and License information:  ©2020, Contat et al
This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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