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I have two samples A and B and I do have an RNAseq for both of them. Inside each file (for A and B) I do have a set of FPKMs that give me a fold change for each gene (sample vs control). It looks somewhat like that:

gen_name grp01 grp02 grp03 grp04 fold_change
gene1    10    10    5     5     2
gene2    11    11    11    11    1
gene3    5     5     10    10    0.5
gene4    ... 

for sample A and, say

gen_name grp05 grp06 grp07 grp08 fold_change
gene1    100   100   5     5     20
gene2    110   110   110   110   1
gene3    5     5     100   100   0.05
gene4    ... 

for sample B

I need to show with PCA that, foe example, gene1 is sample B is much more overexpressed than in sample A, same for gene3, but it looks like gene2 is not very interesting.

What data must be put in PCA analysis?

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    $\begingroup$ Using a package is the best approach. Scanpy is popular right now. I do this stuff via first principles, so my advice isn't cool here. Anyway, I'd combine all data into one dataframe, minus log-fold change. I assume log fold change is the opposing sample? The data must have a column to identify A genes from B genes, or denoted within the gene name. PCA does not give gene by gene comparisons, it will be cluster by cluster. Interpreting each clusters is done independently (by mapping the log-fold-change), i.e. what is clustering together and that cluster represents a cohesive expression group. $\endgroup$
    – M__
    Commented Mar 10, 2023 at 1:36
  • $\begingroup$ The alternative is DEG analysis, gene by gene - which you've already done. $\endgroup$
    – M__
    Commented Mar 10, 2023 at 1:50
  • $\begingroup$ Thank you. I want to show that A is different from B based on an expression of gene1 and gene3 (in this test experiment). I want to do this in R but scanpy is a python package. Is there any way to use prcomp() ? $\endgroup$
    – Lara
    Commented Mar 10, 2023 at 3:43

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