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sr320 / ceabigr

Workshop on genomic data integration with a emphasis on epigenetic data (FHL 2022)
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examine potential for ASCA for exon analysis #90

Closed sr320 closed 3 months ago

AHuffmyer commented 4 months ago

AH moving to this next - WGCNA presents some barriers as noted in issue #91

AHuffmyer commented 4 months ago

Trying the ALASCA package: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645785/ with info here https://andjar.github.io/ALASCA/articles/ALASCA.html. Looks promising!

AHuffmyer commented 4 months ago

Genes for ground truthing

List of 6 genes from PC1 (linear decreasing trend; no difference between treatment)

List of 6 genes from PC5 (higher in control and lower in exposed)

AHuffmyer commented 4 months ago

PC1 looks like this from ASCA:

Screenshot 2024-03-06 at 13 37 14

PC5 looks like this from ASCA:

Screenshot 2024-03-06 at 13 37 02

AHuffmyer commented 4 months ago

List of 6 genes from PC6 (opposite pattern of increase/decrease)

Screenshot 2024-03-06 at 13 42 13

AHuffmyer commented 4 months ago

AH to do: Generate figure panel for each PC, add scree plot and model stats, generate list of top 10 genes in each PC.

AHuffmyer commented 3 months ago

Results added to manuscript document and figures uploaded to repo

AHuffmyer commented 3 months ago

Notebook post with analysis: https://ahuffmyer.github.io/ASH_Putnam_Lab_Notebook/Analysis-of-Variance-Simultaneous-Component-Analyses-ASCA-for-CEABIGR-project/