Differential transcript usage StageR error message

Question

[akilabioinfo]

Dear All,

I have used the recent protocol for DTU analysis from this recent version

I am facing some issues while doing the stagewise analysis for dtu

stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmation, pScreenAdjusted=TRUE, tx2gene=tx2gene)
stageRObj <- stageWiseAdjustment(object=stageRObj, method="dtu", alpha=0.05)

Error in .stageWiseTest(pScreen = pScreen, pConfirmation = pConfirmation,  : 
NA p-values found in either the screening or confirmation tests.

If you want to allow for NA p-values, set allowNA = TRUE.

If I give allowNA = TRUE it is showing like this:

stageRObj <- stageWiseAdjustment(object=stageRObj, method="dtu", alpha=0.05, allowNA=TRUE)
Removing 4 features with NA screening hypothesis p-values. 

Error in pConfirmation[id, ] : incorrect number of dimensions

Help me

[zx8754]

It is something to do with dimension of your input datasets, check dim(pScreen), dim(pConfirmation), check the example datasets dimensions. Ensure str() of your data is same as example datasets, etc. Joys of debugging.