Mayo Clinic RNA-Seq Analysis

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Mayo Clinic RNA-Seq Analysis

Postby cpere117 » Thu Mar 11, 2021 1:50 pm

Dear SMLG Members,

I'm working on a mayo clinic RNA-Seq cohort where datasets I've compiled are derived from three separate labs. In the attachment you can find the raw data from each of these three separate labs, annotated by ensemble ID. If you can help me with the normalization of this data from across three datasets I would be greatly appreciative. The Dr. Taner dataset attached represents Cerebellum data from 200 Cerebral Amyloid Angiopathy Cases derived from this synapse repository: https://www.synapse.org/#!Synapse:syn10930230. The Dr. Bu dataset attached represents Temporal Cortex data from 75 Cerebral Amyloid Angiopathy Cases. Lastly, my Control dataset attached represents data from the Mayo-Clinic AD Cohort and can be found in this synapse repository: https://www.synapse.org/#!Synapse:syn5550404. I would like to see what would be best to normalize this data. I've normalized the data according to the Trim Mean Normalization method across all three separate datasets. I'm interested to see any other normalization methods that can help me compare cases and controls between these three studies. Thank you.

CP
Attachments
MayoRNAseq_RNAseq_TCX_covariates_Check.csv
Mayo-RNA Seq Control Temporal Cortex Samples Metadata
(22.72 KiB) Downloaded 99 times
MayoRNAseq_RNAseq_CER_Check.csv
Mayo-RNA Seq Control Cerebellum Samples Metadata
(21.93 KiB) Downloaded 113 times
MC-CAA_individual_human_metadata.csv
Metadata for the Dr. Bu and Dr. Taner Patients
(67.32 KiB) Downloaded 98 times
Mayo-RNA-Seq Controls_ Study Three.xlsx
Mayo-RNA Seq Controls
(74.21 MiB) Downloaded 105 times
Dr. Bu MC-CAA Raw Counts .xlsx
Dr. Bu CAA Temporal Cortex Cases
(19.79 MiB) Downloaded 107 times
Dr. Taner MC-CAA Raw Dataset .xlsx
Dr. Taner CAA Cerebellum Cases
(20.03 MiB) Downloaded 108 times
cpere117
 
Posts: 38
Joined: Thu Aug 24, 2017 7:15 pm

Re: Mayo Clinic RNA-Seq Analysis

Postby cpere117 » Tue Sep 28, 2021 6:13 pm

Dr. Yoo,

Attached is the excel file on how I cleaned the Mayo clinic data for Banjo. The 313 genes represent ID3 targets of interest and clinical variables derived from the Mayo clinic data from my original post. To the left of the spreadsheet is the raw counts of the data. In the second step, I log2 transformed the data to assure normalized distribution. I then calculated the mean and standard deviation of the log2 transformed data. Using the (log2 transformed expression value - the mean log2 expression value)/ standard deviation of the log2 transformed gene expression value I calculated the Z scores for each of my genes across 73 samples. The last data matrix in the sheet to the right is the discretized values based on the Z scores ( 0 (< -1 Z score), 1 (Between -1 to 1 Z score), 2 (> 1 Z score)).

Christian

@cwyoo
Attachments
ID3 ENCODE FEMALE CAA TCX BANJO ZSCORE to Discretization .xlsx
(2.05 MiB) Downloaded 95 times
cpere117
 
Posts: 38
Joined: Thu Aug 24, 2017 7:15 pm

Re: Mayo Clinic RNA-Seq Analysis

Postby cpere117 » Tue Oct 19, 2021 1:05 pm

Dr. Yoo,

Attached is the excel file on how I cleaned the Mayo clinic data for Banjo. The 290 genes represent NRF1 targets of interest and clinical variables derived from the Mayo clinic data from my original post. To the left of the spreadsheet is the raw counts of the data. In the second step, I log2 transformed the data to assure normalized distribution. I then calculated the mean and standard deviation of the log2 transformed data. Using the (log2 transformed expression value - the mean log2 expression value)/ standard deviation of the log2 transformed gene expression value I calculated the Z scores for each of my genes across 80 Male samples. The last data matrix in the sheet to the right is the discretized values based on the Z scores ( 0 (< -1 Z score), 1 (Between -1 to 1 Z score), 2 (> 1 Z score)).

Christian
Attachments
NRF1 ENCODE MALE CAA TCX BANJO.xlsx
(1.71 MiB) Downloaded 91 times
cpere117
 
Posts: 38
Joined: Thu Aug 24, 2017 7:15 pm


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