Hi,
I downloaded TCGA data using R TCGABiolinks framework.
The LUAD clinical dataset has a variablepaper_iCluster.group
, I've found this resource TCGA_Marker_Papers, which says that all the variables starting by paper_
come from PanCancerAtlas publications. I've tracked down the origin of this variable to the following paper LUAD.
For LUSC a similar paper exists LUSC, which also makes reference to the classification of this iCluster.group however I don't have this variable in my lusc clinical dataset.
I wonder if someone who has worked with this datasets already knows if there is a way of getting this classification for the lusc dataset. I also suspect this might be a data inconsistency from downloading the data from TCGABiolinks.
Any help is appreciated,
Thanks in advance
If it's not at the GDC Data Portal or the GDC Legacy Archive, then I am doubtful that you will find it anywhere. But you are welcome to continue to search.
Hint: filter for 'clinical' (under Data Category) and 'bcr biotab' or 'Biotab' (under Data Format).
Kevin
Hi Kevin,
The classification is provided in the luad paper in the supplementary data section and on the lusc paper not. I'm not sure if it was forgotten by lapse, because the same methodology was applied and the paper also references performing integrative clustering, the figures showing the iClusters are present on the supplementary figures but not on the data.
I've emailed the corresponding author, so maybe I'll get to know where it is.
I appreciate the help,
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