is "median expression" that has a RSEM value represent FPKM units?

[wcharle...@gmail.com]

in other words - is the TCGA expression data (expression_median and not z-scores) in FPKM units?

[JJ Gao]

Hi William,

Are you looking at the data files from datahub?

The data in data_RNA_Seq_expression_median.txt (profile id ending with rna_seq_mrna) are RPKM data.

The data in data_RNA_Seq_v2_expression_median.txt (profile id ending with rna_seq_v2_mrna) are RSEM data (normalized_results).

-JJ

On Tue, Feb 26, 2019 at 4:45 PM <wcharle...@gmail.com> wrote:

in other words - is the TCGA expression data (expression_median and not z-scores) in FPKM units?

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[Sivasish Sindiri]

Hi JJ,

"The data in data_RNA_Seq_expression_median.txt (profile id ending with rna_seq_mrna) are RPKM data  " : Does it mean that the data was downloaded from TCGA and raw files were processed using TCGA Pipeline or by the method used by the authors of that particular study? 

[mohammed imran Khan]

Please follow this link from Jianjiong Gao.

It might be very helpful. 

https://groups.google.com/g/cbioportal/c/_GqHcYT2jac/m/x_W0B2EICQAJ

Best regards--

Imran

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/367f912c-2150-463e-83eb-2c16db56d78cn%40googlegroups.com.

[Sivasish Sindiri]

I saw this link but it doesn't have information about " data_RNA_Seq_expression_median.txt  " files. 

[Sivasish Sindiri]

I see the file  " data_RNA_Seq_expression_median.txt  " has discrete data and not continuous (usually RPKM/FPKM values are floats). Are you sure the expression is in RPKM and not raw read count? If its RPKM data, has it been rounded to make it discrete?