Question: DEXseq plot, determin the EU Fold change
gravatar for layal8785
6 months ago by
layal87850 wrote:

In "plotDEXseq" function, we can provide the FDR and other few arguments as normalized counts, names, ... 

The  significant differential used exon  shows as a red bar.
but I want to visualize as significant just the exons which passed my adjusted P-value and log2FoldChange thresholds
for example I put a threshold as
padj < 0.01
log2fold_condition1_condition2 > 2 (Fold change of 4)

How to pass this parameter to the "plotDEXseq" function ? Shall I subset the DEXSeqDataSet object according to my criteria?

ADD COMMENTlink modified 6 months ago • written 6 months ago by layal87850

Hi, currently there is not a parameter for this, but I can add that to my todo list. In the meantime, what you could do is to set the adjusted p-values to 1 whenever the fold changes are lower than your threshold (only for the purposes of visualization). 

ADD REPLYlink written 6 months ago by Alejandro Reyes1.5k
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