Zinc & Aging part II Genetic Data

Zinc & Aging part II Genetic Data

Postby rpazo001 » Sun Feb 26, 2023 1:46 pm

FASTQC Reports for Trimmomatic Data
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Re: Zinc & Aging part II Genetic Data

Postby rpazo001 » Sun Feb 26, 2023 1:48 pm

Multi QC
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Re: Zinc & Aging part II Genetic Data

Postby rpazo001 » Sun Feb 26, 2023 1:51 pm

Feature Count Data Plus Graphs ( Multi QC)
Taabular Count Data
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MultiQC_From Featured Counts.zip
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Multi_QC_Featured_Counts.xlsx
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Re: Zinc & Aging part II Genetic Data

Postby rpazo001 » Mon Mar 27, 2023 6:24 pm

Data for BANJO

Sheet one contains participant ID in the first column, I ( for intervention in the second column) with B= Baseline and F= Fasted, the rest of the columns are the genes ( There are 350 gene columns total).

Sheet two contains the data in an easier way to input it into BNLEARN. The 350 genes come first and then the intervention data is in the last column.

Gene discretization key:
low = low expression; z<-1
none = no signficant gene expression; (-1 ≤ z ≤ 1)
high = high expression; z >1
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Intervention3_27.xlsx
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Re: Zinc & Aging part II Genetic Data

Postby rpazo001 » Mon Mar 27, 2023 6:39 pm

Gene Expression Data
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Data_F.xlsx
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Re: Zinc & Aging part II Genetic Data

Postby rpazo001 » Mon Apr 10, 2023 6:31 pm

Data normalized by z score (see d-scale)
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d_scale.xlsx
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Re: Zinc & Aging part II Genetic Data

Postby rpazo001 » Mon Apr 10, 2023 7:11 pm

R script is posted in github

https://github.com/smlgfiuedu/BNLEARN-G ... ta-anlysis

Network scores generated :
> score(Bn4, Intervention, type = "bde" )
[1] -7082.487
> score(Bn4, Intervention, type = "loglik")
[1] -2544.214
> score(Bn5, Intervention, type = "bde" )
[1] -7095.455
> score(Bn5, Intervention, type = "loglik")
[1] -2592.736
> score(Bn6, Intervention, type = "bde" )
[1] -7101.518
> score(Bn6, Intervention, type = "loglik")
[1] -2555.251
> score(Bn7, Intervention, type = "bde" )
[1] -7095.455
> score(Bn7, Intervention, type = "loglik")
[1] -2592.736
> score(Bn8, Intervention, type = "bde" )
[1] -7095.455
> score(Bn8, Intervention, type = "loglik")
[1] -2592.736
>
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Re: Zinc & Aging part II Genetic Data

Postby rpazo001 » Wed Apr 12, 2023 6:27 am

CounT data

First column is Gene ID prior to annotation
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Countdata.csv
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Last edited by rpazo001 on Wed Apr 12, 2023 6:33 am, edited 1 time in total.
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Re: Zinc & Aging part II Genetic Data

Postby rpazo001 » Wed Apr 12, 2023 6:31 am

DESSEQ2 Count Normalization ( See script posted in github)
https://github.com/smlgfiuedu/DESEQ-2-d ... ptDeseq2.R

DESEQ2 Count Normalization Method:
1) Determine Estimates Size Factor
2) Create Normalized Object
3) Undergo Variance Stablization Transformation

https://www.bioconductor.org/packages/d ... sformation
https://hbctraining.github.io/DGE_works ... ation.html
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Re: Zinc & Aging part II Genetic Data

Postby cwyoo » Mon Apr 17, 2023 12:00 pm

rpazo001 wrote:CounT data

First column is Gene ID prior to annotation


Can you post a count data with gene names annotated?
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