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saezlab / MetaProViz

R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
https://saezlab.github.io/MetaProViz/
GNU General Public License v3.0
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MetaProViz::Preprocessing QC plots #61

Closed ChristinaSchmidt1 closed 11 months ago

ChristinaSchmidt1 commented 1 year ago

After some discussions I think we should consider to add some more QC plots:

  1. RLA plot before and after normalisation (of course if no normalisation =TIC is done, than just the standard plot) image
  2. Additional PCA plot with pool samples and/or blank samples (if CoRE=TRUE).
dprymidis commented 12 months ago

Added PCA for pool samples in the Pool_Estimation function

If all data are used as input: image

If Only pool samples were used image

PCA for CoRe Media samples in already in there.

For the RLA, I am not sure if what I did is correct ( based on this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544854/, I did the following) :

  1. log transform the data
  2. got the median for each sample
  3. subtracted the median from all the values for each sample.
  4. make boxplots for each sample
  5. Put boxplots (before and after norm) together
image
ChristinaSchmidt1 commented 12 months ago

Great, thanks!

Yes, I think this is exactly how an RLA-ploy is done. If the user has provided conditions we can colour code the boxplots for conditions (no need for a legend of this thow).

FYI: There is another issue I opened where I posted about QC plots for Pool_Estimation, where I added two additional plots we could use as well.

dprymidis commented 12 months ago

This is done

ChristinaSchmidt1 commented 11 months ago

I am just going trought he open issues and I think this one is complete (?). If yes, could you confirm and close the issue?