Signaling in PC3 and PC4

Question

[shangyuan5000]

Hi, I have for group conditions and I run PCA analysis in DESeq2. After trying different PCs in the PCA plot, I found that PC3 and PC4 plot could well separate my samples: https://ibb.co/d5mpHn

I think that means my signaling probably mainly located in the PC3&PC4 directions, while PC1 and PC2 are just some other un-relevant things. In this case, is there any tricks to let me focus on the signal I wanted? Or is there any papers discussing this issues? I think this phenomenon is quite common in RNA-seq analysis.

Best regards, Raymond

Answer 1

[Kevin Blighe]

Hi Raymond / shangyuan5000

That looks quite convincing. Essentially, PC3 separates M from F, whilst PC4 separates 3 from 4. What do PC1 an PC2 separate?

What you need to do next is derive the rotated component loadings (or 'variable loadings') to each PC, and then order each of these by absolute value.. These loadings indicate the strength of each gene to each PC, i.e., the amount of variation that the gene contributes to each PC.

Following my example here ( A: PCA plot from read count matrix from RNA-Seq ), the project.pca object will contain the rotated component loadings data structure, amongst many other structures. Look up the prcomp function to see how you can access these.

Kevin

[shangyuan5000]

Thanks, Kevin. My PC1 and PC2 does not separate the samples by groups, and I have no idea what they are separating since all samples were coming from the same batch as I was told. I will follow your example first and see what's coming out. To look into the loadings seems to be a really good idea. Thanks very much!. PC1 and PC2