Help! data_mrna_seq_v2_rsem_zscores_ref_all_samples

[Luisa Quesada]

Hi, 

I'm having issues finding a clear answer or description of how this data was normalized: data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt

I have read multiple resources and a lot say something different. Could you provide a clearer explanation? 

Some resources say it's been log2(raw_counts + 1) transformed, but others say it has been divided by the 75th percentile and then multiplied by 1000. 

Are you doing both of these? 

1. Division by 75th percent and multiplying by 1000. Giving Result1

2. log2 (Result1 + 1). Giving Result2
3. z-score (Result2 - mean(Result2))/std(Result2)

I'm not sure if the data I'm downloading already includes all of these steps or if I should perform some normalization after? 

I'm mainly concerned about not knowing if it was log normalized because of some calculations that I'm doing which could impact the interpretation of the results.

Thank you in advance, 

Luisa Quesada

Graduate Research Assistant

Biomedical Engineering

Fallahi-Sichani Lab 

University of Virginia 

Pronouns: She/her/hers