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WWXkenmo / ENIGMA

A fast and accurate deconvolution algorithm based on regularized matrix completion algorithm (ENIGMA)
MIT License
27 stars 6 forks source link

Error in rep(value, length.out = nrows) : #1

Closed peachone closed 3 years ago

peachone commented 3 years ago

attempt to replicate an object of type 'S4' Thank you so much for uploading such a great tool, but I'm having problems using a as a reference. I managed to common Create ENIGMA object, but got an error when running the mode batch effect correction.

It seems that I have a problem with my reference, but my reference is a single cell data of 7 cell types.Here is my code situation, I would be grateful if you could help me .

mode batch effect correction
+   egm = batch_correct(egm, 
+                       varname_cell_type = "cellType", 
+                       n_pseudo_bulk=100)

Tue Sep 28 11:28:58 2021 Reference is from Single Cell RNA-seq, doing batch correction in S mode. Tue Sep 28 11:28:58 2021 Generating pseudo bulk... Tue Sep 28 11:29:24 2021 Doing ComBat... Found 693 genes with uniform expression within a single batch (all zeros); these will not be adjusted for batch. Found2batches Adjusting for0covariate(s) or covariate level(s) Standardizing Data across genes Fitting L/S model and finding priors Finding parametric adjustments Adjusting the Data

Tue Sep 28 11:29:27 2021 Restore reference... Error in rep(value, length.out = nrows) : attempt to replicate an object of type 'S4'

WWXkenmo commented 3 years ago

Thx for using our tool! I would check the source code later I just want to maker sure that are you using the v1.1 version or just originally version, I gonna check later

peachone commented 3 years ago

@WWXkenmo Thanks for the reply, I've re-run it now and it's ok.

WWXkenmo commented 3 years ago

Okey! I really want hear the feedback from the user, if you encounter any questions about usage and analytic results interpretation, contact with me please!