Originally posted by super0925
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On top of this, I am thinking of doing a normalization of the counts to see how the data appears in normalized data sets. I will be using the Benjamini-Hochberg false discovery rate of 0.01 for EdgeR based on a recent paper . I am going to apply the same principle on DeSEQ as well.
Overall goal is to illustrate that these three genes based on three independent RNA-Seq Analysis tools yield the same results of these certain genes are being highly expressed in Organ A versus Organ B. I am working on other in situ models and analysis to indicate that these genes share a common expression.
Also I created the counts using HTSEQ.
Originally posted by sindrle
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Source for EdgeR: http://rnajournal.cshlp.org/content/....DC1/edgeR.pdf
Thank you again for all the great help.
Where exactly the confidence intervals, SD, Dispersion estimates in the Cuffdiff output files?
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