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Thank you again, finally we decided to exclude these samples from the analysis!
I have only last question for you about interpreting the results.. when I make the MAplot of a comparison, how do I know what level is represented by the red line?
For example:
res2 <- results(dds,contrast=c("condition","V1","V2"))
resOrd_res2 <- res2[order(res2$padj),]
plotMA(resOrd_res2,alpha=0.05,main="1A vs. 1B",ylim=c(-3,3))
In V1 vs V2 comparison I found 1 miRNA DE, that is represented (by a red point) in MAplot below the red line.
Is this miRNA under-expressed in the Variant 1 with respect to the Variant 2 (then V2 is the red line), or vice versa?
I have only last question for you about interpreting the results.. when I make the MAplot of a comparison, how do I know what level is represented by the red line?
For example:
res2 <- results(dds,contrast=c("condition","V1","V2"))
resOrd_res2 <- res2[order(res2$padj),]
plotMA(resOrd_res2,alpha=0.05,main="1A vs. 1B",ylim=c(-3,3))
In V1 vs V2 comparison I found 1 miRNA DE, that is represented (by a red point) in MAplot below the red line.
Is this miRNA under-expressed in the Variant 1 with respect to the Variant 2 (then V2 is the red line), or vice versa?
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