cummeRbund MDS and PCA plot explanation

[Sushil]

Hello folks,

I have limited understanding of RNA seq data analysis. I am using cufflink pipeline to analyse my RNAseq data comprising 1 treatment and 1 control. Three biological replicates in each condition. Can anybody help me whether I should trust my data based on the MDS plot? Any other suggestion to correct if there are any biases in the sample?

Thanks
Sushil

[danwiththeplan]

I'm not an expert but if your replicates are closer to replicates from another condition than they are to each other, I can see a problem. Surely replicates from a single condition should cluster?