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Old 01-24-2015, 08:08 AM   #1
Sushil
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Default 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?

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Sushil
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Old 07-29-2015, 08:07 PM   #2
danwiththeplan
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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?
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