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DarrianTalamantes / QPCR_Data_Wrangler

Various Things to help with a roche 480 data output
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Biomass Analysis #2

Open DarrianTalamantes opened 1 month ago

DarrianTalamantes commented 1 month ago

This project is all about analyzing the biomass estimation and alkaloid data.

DarrianTalamantes commented 1 month ago

Making graphs

Graph that shows endophyte ng dna vs fescue ng dna

Here we see a large separation between plate 1 and plate 2.

https://github.com/DarrianTalamantes/QPCR_Data_Wrangler/blob/fcea4970b5f7c2254caec30ce591520bb719afa5/Program/Biomass_analysis_2024.R#L52C1-L55C13 FescueVsEndo

Graph that shows Endophyte/Fescue vs alkaloid ppb

There seems to be little to no correlation https://github.com/DarrianTalamantes/QPCR_Data_Wrangler/blob/fcea4970b5f7c2254caec30ce591520bb719afa5/Program/Biomass_analysis_2024.R#L57C1-L63C13 alkaloid_biomass_correltation

DarrianTalamantes commented 1 month ago

These two graphs are the same ones from before but I added the third and final plate for the Biomass analysis.

Alkaloid_vs_Endophyte Endo_TF_DNA

DarrianTalamantes commented 3 weeks ago

Fixed a previous graph r squared

Alkaloid_vs_Endophyte

DarrianTalamantes commented 3 weeks ago

Removed batch effect.

I did this by running a linear model. The model used plate as a function of delta CT. This gives us residuals. These residuals will be the all the error thats not the plate. I added the mean of the delta CT to the residuals and plotted them.

Alkaloid_vs_Endophyte_removed_batch_effect