HTSeq - Counts, HTSeq - FPKM, HTSeq - FPKM-UQ?

[Katie Dunphy]

Hi all,

I am new to UCSC Xena and RNA seq data so this may be a simple question. I have a protein list and I want to see if the gene expression of these proteins associate with survival using Kaplan Meier Curves and MMRF CoMMpass dataset. Which type of data is most suitable for visualizing the Kaplan Meier curves on Xena - HTSeq - Counts, HTSeq - FPKM or HTSeq - FPKM - UQ? Or is manual normalization of the data required?

Thank you for your help,

Katie.

[Mary Goldman]

Hi Katie,

They should all be similar for the analysis that you're doing. Choose whatever one you prefer.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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[Katie Dunphy]

Hi Mary,

Thank you for your help :) I've just compared some of the significance values for the HTSeq - Counts and HTSeq - FPKM -UQ and got the attached list. Some of the values are quite different and I'm not sure if it correct for me to say that certain gene expressions are prognostically significant when they are significant when using the HTSeq - Counts but not for the HTSeq - FPKM -UQ? Sorry to bother you again and thank you for the help!

All the best,

Katie.

[Mary Goldman]

Hi Katie,

I would recommend contacting the GDC directly as this is where this data originates: https://gdc.cancer.gov/support.

Best,

Mary

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