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kkang7 / CDSeq_R_Package

CDSeq R Package
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length(gene_length) should be equal to nrow(bulk_data) #14

Open nbutyrate opened 2 years ago

nbutyrate commented 2 years ago

Hi I tried the following

          result2<-CDSeq(bulk_data =  M2, 
          cell_type_number = 2:10, 
          mcmc_iterations = 5, 
          dilution_factor = 1, 
          block_number = 1, 
          gene_length = as.vector(gene_length), 
          reference_gep = refGEP, # gene expression profile of pure cell lines
          cpu_number = 1, # use multiple cores to save time. Set the cpu_number = length(cell_type_number) if there is enough cores.
          print_progress_msg_to_file = 0)

and got the following error

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 CDSeq(bulk_data = M2, cell_type_number = 2:10, mcmc_iterations = 5, : length(gene_length) should be equal to nrow(bulk_data)

my data looks like

head(M2) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [1,] 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 [3,] 94 101 92 126 213 263 515 99 173 107 180 301 109 185 130 52 203 84 118 170 [4,] 8 7 8 10 24 16 20 11 12 7 8 15 9 11 10 13 13 14 6 23 [5,] 25 34 26 27 64 66 114 32 73 46 42 52 38 70 68 43 73 47 40 59 [6,] 2 6 6 7 0 5 6 3 4 4 3 12 2 8 5 4 5 6 3 5 [,21] [,22] [,23] [,24] [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38] [1,] 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 [2,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [3,] 188 132 481 173 103 116 163 183 198 149 131 89 225 150 226 160 586 657

kkang7 commented 2 years ago

Sorry for late response. Is your M2 of dimension gene by sample? Also, mcmc_iterations = 5 won't converge, try 1000 or something.