Error in runAutoencoderDenoising

[p-lombard]

Hi! I seem to be running into a persistent error with runAutoencoderDenoising:

Error in [[<-.data.frame(*tmp*, mtr_name, value = list(df = list(genes = c("AL627309.1", : replacement has 3 rows, data has 36478

I've tried different SPATA objects but can't seem to get around this issue. runAutoencoderAssessment() works fine.

R version 4.3.3 (2024-02-29 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64

[p-lombard]

After looking through the scripts in the github, it appears that the error is being thrown when addGeneMetaData() is called. Line 711 in add.R is causing the error in addGeneMetaData).

object@gdata[[of_sample]][[mtr_name]] <- meta_data_list

• For my SPATA object, object@gdata[[of_sample]] contains a 36478 x 8 dataframe while meta_data_list is a 3 item list containing a df with the denoised data
• Even if meta_data_list$df were to be specified when adding the denoised data to gdata (e.g., object@gdata[[of_sample]][[mtr_name]] <- meta_data_list$df) , object@gdata[[of_sample]] is still 36478 x 8 while meta_data_list$df is 24724 x 11, so the same error would occur.

It seems the information being stored in the gdata slot has been changed in the SPATA2 update, which explains why my old SPATA objects don't have this issue. I think the location to which addGeneMetaData saves meta_data_list may need to be changed to reflect this.

Thanks!!

[simonmfr]

Hi @p-lombard, thank you for looking into this, we will get back to you!