error when combining two matrices

[sylestiel]

Hi @rcorces

When combining the GeneScoreMatrix with the Motif Matrix using the script
trajCombined <- trajGSM2
assay(trajCombined) <- t(apply(assay(trajGSM2), 1, scale)) + t(apply(assay(trajMM2), 1, scale))

I encounter the error that reads as follows:
Error in assays<-(*tmp*, withDimnames = withDimnames, ..., value = *vtmp*) :
please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x, withDimnames=FALSE))
<- value' when the rownames or colnames of the supplied assay(s) are not identical to
those of the receiving SummarizedExperiment object 'x'

Can you suggest a way to modify the script to prevent this error?

The trajectory heatmap of the combined matrices are plotted with no problem but the recurrence of this error is bothersome.

Thanks!

[rcorces]

have you tried doing what the error suggests?

assay(trajCombined, withDimnames = FALSE) <- t(apply(assay(trajGSM2), 1, scale)) + t(apply(assay(trajMM2), 1, scale))

[sylestiel]

Okay. That worked. Why was that necessary?

[rcorces]

as the error says, this is required when:

when the rownames or colnames of the supplied assay(s) are not identical to those of the receiving SummarizedExperiment object 'x'

[sylestiel]

Thanks!