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vyepez88 avatar vyepez88 commented on July 17, 2024

That corresponds to a non-standard chromosome. Counting the split reads in those can lead to errors. For that reason we included the parameter keepNonStandardChrs in the aberrant splicing dictionary. Set it to false and the non-standard chromosomes will not be counted.

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gevro avatar gevro commented on July 17, 2024

Thanks. FYI - that is not in the documentation.

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projectoriented avatar projectoriented commented on July 17, 2024

Hello,

I'm receiving a similar error but it's from AE module instead.

ods <- readRDS("output/processed_results/aberrant_expression/v34/outrider/blood/ods_unfitted.Rds")
implementation <- "autoencoder"
register(MulticoreParam(3))

## subset filtered and estimate
ods <- ods[mcols(ods)$passedFilter,] 
ods <- estimateSizeFactors(ods)

## find optimal encoding dimension
a <- 5 
b <- min(ncol(ods), nrow(ods)) /20  # N/3

maxSteps <- 15

Nsteps <- min(maxSteps, b) 

# Do unique in case 2 were repeated
pars_q <- round(exp(seq(log(a),log(b),length.out = Nsteps))) %>% unique
ods <- findEncodingDim(ods, params = pars_q, implementation = implementation)
> ods <- findEncodingDim(ods, params = pars_q, implementation = implementation)
Wed Apr 14 10:46:04 2021: SizeFactor estimation ...
Wed Apr 14 10:46:05 2021: Controlling for confounders ...
Wed Apr 14 10:46:05 2021: Using the autoencoder implementation for controlling.
[1] "Wed Apr 14 10:46:13 2021: Initial PCA loss: 54.7283190258117"
Error: BiocParallel errors
  element index: 1
  first error: L-BFGS-B needs finite values of 'fn'
In addition: Warning message:
stop worker failed:
  attempt to select less than one element in OneIndex 

There are 158 samples (blood) for this AE run and I've tried different mp sizes to narrow down the search parameter but am still receiving this error- help! :'(

@mumichae @vyepez88

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projectoriented avatar projectoriented commented on July 17, 2024

Apologies for the spam, I'm just seeing this issue: gagneurlab/OUTRIDER#25 & will try to resolve from there

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vyepez88 avatar vyepez88 commented on July 17, 2024

keep us updated

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