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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? -
cummeRbund MDS and PCA plot explanation
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
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM
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