Hello again @MarkoTerzin!
is sPLS the best option analysis to use?
By the sounds of experimental design, sPLS and multilevel sPLS are going to be your best bet. You could also explore rCCA (read more here and here).
Out of curiosity, what are the dimensions of your datasets? How many missing values are there?
I am always getting that 2PCs is the optimal number to retain
Regarding this comment and your interpretation: I’ve seen many cases where 2 components was more than sufficient for a given analysis. However, without your results its hard to say. I would encourage you to explore the explained variance of each component and the loadings (feature contributions) to each component to determine whether this model is valid. If you want me to go more in depth regarding this, just say the word
How can I fix the coloring scale when making the heatmap
I’m surprised I haven’t seen someone asking about this before - this seems like a useful feature. I’ll add it to my list! You can set symkey to FALSE (see ?cim) which will not force the key to be symmetric. This may help with the colouring slightly. Otherwise, I’ll keep you updated regarding the implementation of a way to properly control the scale.
stratified CV approach – how can I apply this CV method
I’ve just realised that interestingly, only the SPLS-DA methods apply stratified sampling using the classes of each sample. Stratifying the subsamples by the repeated measurements would be handy. I’ll also look into a implementation of this for multilevel sPLS.
Is there any additional advice when working with microbial data in particular?
I’m not an expert when it comes to microbial data. Pretty much everything I can speak to is contained on the site. This includes the three primary steps of pre-processing covered here.
Having a bit of a look online, I found this page which may be of use. I also found a python repository and accompanying paper which you could reverse engineer to some extent.
I will attend your course in November
Fantastic to hear! Regarding the internships, I’ll ask A/Prof Lê Cao as she’ll know - I wasn’t even aware we did!
Hope this info dump is helpful
Cheers,
Max.