[cbioportal] about mRNA Expression z-Scores (RNA Seq V2 RSEM)

[JJ Gao]

Hi Luisa,

Yes, we log transformed the data before calculating zscore in data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt as indicated in the metadata file: meta_mrna_seq_v2_rsem_zscores_ref_all_samples.txt.

Please let us know if you have any additional questions.

Best,

-JJ

ps. It would be great if the support group can be added in future emails so that other users can benefit from the questions and answers. Thanks!

On Thu, Aug 18, 2022 at 2:17 PM Luisa Quesada <lu.qu...@gmail.com> wrote:

Hi Jianjiong, 

I've tried to go through different resources about normalized_count normalization. I understand that it's raw_counts/75th percentile * 1000, are they log2 transformed after? 
I'm using your data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt data and I'm wondering if these include a log transform because it will affect the way I interpret the relationship between the expression (if I want to add or subtract etc)

thank you!

Luisa

On Saturday, June 16, 2018 at 7:34:56 PM UTC-4 Jianjiong Gao wrote:

HI Aron,

The z scores are based on the normalized_count (RSEM): https://www.biostars.org/p/106127/

Thanks,

-JJ

On Thu, Jun 14, 2018 at 10:10 AM <ayc...@gmail.com> wrote:

Hi,

Are the z scores calculated for each gene based on raw counts? normalized count? TPM or FPKM (from RSEM)?

Thanks

Aron

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