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Lots of people also do grid plots of Pearson/Spearman correlation, sometimes with a hierarchically clustered dendrogram on the axes. Also easy to do in R with the cor() function once you have a matrix of genes by samples.
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You can also just do a scatter plot, for example in R, of Rep1 vs Rep2. This can be a bit easier to understand when communicating your results to other researchers.
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Originally posted by jake13 View PostHi,
I'm new to RNA-seq analysis. I have biological duplicates of 4 different conditions. I want to check how good the replicates are for each condition. I have got them mapped to the genome and have run cuffdiff on the files, but I was wondering what comparisons people do/tools people use to check their replicates?
Thanks
Dario
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Check that replicates are good
Hi,
I'm new to RNA-seq analysis. I have biological duplicates of 4 different conditions. I want to check how good the replicates are for each condition. I have got them mapped to the genome and have run cuffdiff on the files, but I was wondering what comparisons people do/tools people use to check their replicates?
ThanksTags: None
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