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sr320 / ceabigr

Workshop on genomic data integration with a emphasis on epigenetic data (FHL 2022)
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Update mixomics analysis #82

Closed AHuffmyer closed 4 months ago

AHuffmyer commented 11 months ago

The mixomics figures and output look amazing Yaamini! Is there anything I can do to help with the correlation analysis for methylation and gene expression?

yaaminiv commented 11 months ago

I haven't been able to successfully tune the analysis yet and would appreciate help! I have the code already scripted here: https://github.com/sr320/ceabigr/blob/main/code/gene-methylation-expression-mixomics.Rmd

I couldn't get the code to run on the R Studio Server and I was convinced I needed to run the code on mox instead. I tried running code on mox but was unsuccessful.

AHuffmyer commented 11 months ago

Great, thank you! I'll take another look at this and see what we can do for tuning. If we can run the analysis using the full data set successfully without the need to tune and reduce input variables then I believe we can proceed without that step. I'll do some research on that as well.

AHuffmyer commented 10 months ago

I am also getting some errors with the tuning stages including Error in Ypred[omit, , h] <- Y.hat[, , 1] : number of items to replace is not a multiple of replacement length. I'll look into this more this week.