Error in CDSeq()

[RK1912]

HI I am using CDSeqR to deconvolve some bulk samples. Hoever I am getting the following error:

res_cdseq = CDSeq::CDSeq(bulk_data = T,cell_type_number = 2:8,cpu_number = 1,mcmc_iterations = 1000, reference_gep = C)
CDSeq is running in non Reduce-Recover mode. To use Reduce-Recover mode, assign a value to block_number that is greater than 1.

Error in { : task 1 failed - "std::bad_alloc"
In addition: Warning messages:
1: In CDSeq::CDSeq(bulk_data = T, cell_type_number = 2:8, cpu_number = 1,  :
  gene_length is NOT provided. CDSeq will estiamte read rate not gene rate. Please provide gene length if you are interested in GEP estimation.
2: In CDSeq::CDSeq(bulk_data = T, cell_type_number = 2:8, cpu_number = 1,  :
  reference_gep is NOT read counts data, RPKM normalization is NOT performed.
3: In CDSeq::CDSeq(bulk_data = T, cell_type_number = 2:8, cpu_number = 1,  :
  Gene length is NOT provided, RPKM normalization is NOT performed.
4: In CDSeq::CDSeq(bulk_data = T, cell_type_number = 2:8, cpu_number = 1,  :
   bulk_data is NOT read count data. Please provide read counts data if possible for potentially better estimations.

I have not provided any gene lengths as I dont have that information, but my data is read counts and not FPKM or any other transformation.

Here is my data: https://github.com/RK1912/Deconv_data

Do let me kwow if I need to make any changes to the data .

Thanks!

[kkang7]

Hi it seems the error is about the memory. Could you try set dulition_factor = 100 and see if you still have the error? and it is okay if you don't have gene length.

Best, Kai

On Tue, Mar 2, 2021 at 1:55 AM Ramya notifications@github.com wrote:

HI I am using CDSeqR to deconvolve some bulk samples. Hoever I am getting the following error:

res_cdseq = CDSeq::CDSeq(bulk_data = T,cell_type_number = 2:8,cpu_number = 1,mcmc_iterations = 1000, reference_gep = C) CDSeq is running in non Reduce-Recover mode. To use Reduce-Recover mode, assign a value to block_number that is greater than 1.

Error in { : task 1 failed - "std::bad_alloc" In addition: Warning messages: 1: In CDSeq::CDSeq(bulk_data = T, cell_type_number = 2:8, cpu_number = 1, : gene_length is NOT provided. CDSeq will estiamte read rate not gene rate. Please provide gene length if you are interested in GEP estimation. 2: In CDSeq::CDSeq(bulk_data = T, cell_type_number = 2:8, cpu_number = 1, : reference_gep is NOT read counts data, RPKM normalization is NOT performed. 3: In CDSeq::CDSeq(bulk_data = T, cell_type_number = 2:8, cpu_number = 1, : Gene length is NOT provided, RPKM normalization is NOT performed. 4: In CDSeq::CDSeq(bulk_data = T, cell_type_number = 2:8, cpu_number = 1, : bulk_data is NOT read count data. Please provide read counts data if possible for potentially better estimations.

I have not provided any gene lengths as I dont have that information, but my data is read counts and not FPKM or any other transformation.

Here is my data: https://github.com/RK1912/Deconv_data http://url

Do let me kwow if I need to make any changes to the data .

Thanks!

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[RK1912]

Hi

Sorry yes, I changed the dilution factor. it is running now but I always get this error at the end.

CDSeq is running in non Reduce-Recover mode. To use Reduce-Recover mode, assign a value to block_number that is greater than 1.

Error in 1:ncol(estGEP) : argument of length 0
Calls: Deconvolution -> <Anonymous> -> paste
In addition: Warning messages:
1: In CDSeq::CDSeq(bulk_data = T, cell_type_number = 2:8, mcmc_iterations = 2000,  :
  gene_length is NOT provided. CDSeq will estiamte read rate not gene rate. Please provide gene length if you are interested in GEP estimation.
2: In CDSeq::CDSeq(bulk_data = T, cell_type_number = 2:8, mcmc_iterations = 2000,  :
  Gene length is NOT provided, RPKM normalization is NOT performed.
3: In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,  :
  scheduled cores 1, 2, 3, 4, 5, 6, 7 did not deliver results, all values of the jobs will be affected
Execution halted

Are the gene lengths compulsory for running cdseq?

Do let me know how I can get around this error.

Thanks !

[kkang7]

Hi @RK1912

Gene length is not compulsory. You can ignore the first two warnings. Could you share some of your data and code so that I can reproduce the error?

[RK1912]

HI Sorry I might have implemented this differently. I am trying to use single cell data as the reference_gep. Is this something that can be done?

[kkang7]

hi @RK1912 Yes, you will need to use the cellTypeAssignSCRNA function to use scRNAseq as reference.