kkang7 / CDSeq_R_Package

CDSeq R Package
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Error in CDSeq() #5

Closed RK1912 closed 3 years ago

RK1912 commented 3 years ago

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!