Question: GDC TCGA LUAD dataset iCluster.group parameter
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gravatar for up201505092
8 weeks ago by
up2015050920 wrote:

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

ADD COMMENTlink modified 8 weeks ago by igor12k • written 8 weeks ago by up2015050920
1

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

ADD REPLYlink written 8 weeks ago by Kevin Blighe69k

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,

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by up2015050920
1

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

ADD REPLYlink written 8 weeks ago by GenoMax95k

See the answer by igor

ADD REPLYlink written 8 weeks ago by Kevin Blighe69k
1
gravatar for igor
8 weeks ago by
igor12k
United States
igor12k wrote:

All the Pan-Cancer Atlas data (which is distinct from the project-specific TCGA datasets/publications) is easily accessible via Xena (iCluster here).

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by igor12k

Hi @igor and thank you for your answer!

The classification in the iCluster link doesn't match the classification I have downloading through TCGABiolinks. Mine is identical to the classification provided in the 'Supplementary Data' section of the LUAD paper I referenced.

I've also browsed Xena and found many cluster classifications, however, I think they are mostly Methylation, mRNA and CNV cluster classifications. The corresponding author has answered and said he was looking for this information and I can update it when I have it.

ADD REPLYlink written 8 weeks ago by up2015050920
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