Recent progress on Proteomics front

  • Can time effect be removed by day * time normalization?
    • scaled all NSAF values by dividing by days * time
    • repeated PCA and ASCA
    • scaling by days * time did not remove the time effect shown by PCA and ASCA time effect analysis
    • PCA shows 29C time points still cluster with

    • IMG

    • temperature seems to be a bigger driver of variance in the time x temperature effect analysis
      • samples cluster more by temperature than by time where before this wasn’t apparent
      • we can look at proteins that show high magnitude loadings values on PC1 to see who’s driving this separation, although for day 7 this doesn’t really hold
      • many proteins differences seem driven by day 3 alone. What do these plots look like if day 3 is removed?
      • now many of the proteins in the higher temperature appear to show the same pattern as the lower temperature only at consistently reduced abundance over time. INTERESTING!