Spam: Biological replicate related problem
We are performing NGS analysis with three biological replicates after analysis results indicate very large FPKM variation in third replicate. For example Control (S1=150, S2=144 and S3=33) while Treatment have shown no variation in the FPKM for example Treatment(S1=1117,S2=1126 and S3=1198). Could anyone suggest me that is this analysis will create problem with fold regulation. We have performed this analysis using trinity(edgeR).
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Dear abhi4.amity, Hi.
Have you performed any PCA or QC Samples and Replicates for your data ?
~ Best
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Are you trying to use a matrix of FPKM as input for edgeR? If yes, you should first read this: Question: normalized FPKM matrix file EdgeR and GO Mapping