EMMCMCStepSummary error

Hi there, I'm encountering the following error when executing the iDEA.fit.

Error in EMMCMCStepSummary(object@summary[, 1], object@summary[, 2], as.matrix(Annot), : pinv(): svd failed

Here is my code.

DEG <- read.table("my_data.csv")
pvalue <- DEG$p_val
zscore <- qnorm(pvalue/2.0, lower.tail=FALSE) #### convert the pvalue to z-score
log2FC <- DEG$avg_log2FC ## effect size
se_beta <- abs(log2FC/zscore)
lfcSE2 = se_beta^2
summary = data.frame(beta = log2FC,beta_var = lfcSE2)
rownames(summary) = rownames(DEG)
> head(summary)
                 beta    beta_var
MGI:1918911 0.2594995 0.008204673
MGI:1913300 0.6050112 0.014540803
MGI:1915609 0.4179491 0.013050508
MGI:1916013 1.0654890 0.053041579
MGI:2152337 0.2732631 0.007393953
MGI:1913456 0.3679529 0.013129402
> nrow(summary)
[1] 2091

data(mouseGeneSets)
> mouseGeneSets[1:3,1:3]
           GO:0000002 GO:0000003 GO:0000009
MGI:101757          0          0          0
MGI:101758          0          0          0
MGI:101759          0          0          0

idea <- CreateiDEAObject(summary, mouseGeneSets, max_var_beta = 100, min_precent_annot = 0.0025, num_core=10)

idea <- iDEA.fit(idea,
                 fit_noGS=FALSE,
             init_beta=NULL, 
             init_tau=c(-2,0.5),
             min_degene=5,
             em_iter=15,
             mcmc_iter=1000, 
             fit.tol=1e-5,
                 modelVariant = F,
             verbose=TRUE)

However, when I try to subset only 4 gene sets, when I create iDEA object. There is no error. (I referenced this page. [https://github.com/xzhoulab/iDEA/issues/21])

idea <- CreateiDEAObject(summary, mouseGeneSets[,c(1,2,13,14)], max_var_beta = 100, min_precent_annot = 0.0025, num_core = 10)
> head(idea@annotation[[1]])
[1]  426  549  552  556  865 1342
> head(idea@annotation[[2]])
[1] 28 33 37 38 57 58
> head(idea@annotation[[3]])
[1]   26   95  191  548  930 1037
> head(idea@annotation[[4]])
[1]  85  90 264 411 586 623

idea <- iDEA.fit(idea,
                 fit_noGS=FALSE,
             init_beta=NULL, 
             init_tau=c(-2,0.5),
             min_degene=5,
             em_iter=15,
             mcmc_iter=1000, 
             fit.tol=1e-5,
                 modelVariant = F,
             verbose=TRUE)

## ===== iDEA INPUT SUMMARY ==== ##
## number of annotations:  4 
## number of genes:  2091 
## number of cores:  10 
## fitting the model with gene sets information... 
  |======================================================================================================================================================================| 100%, Elapsed 00:11

For information, here is my sessionInfo.

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/Soryung/.conda/envs/ENS/lib/libopenblasp-r0.3.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_1.0.7    biomaRt_2.50.3 iDEA_1.0.1    

loaded via a namespace (and not attached):
 [1] KEGGREST_1.34.0        progress_1.2.2         tidyselect_1.1.1      
 [4] purrr_0.3.4            generics_0.1.1         vctrs_0.3.8           
 [7] doSNOW_1.0.20          snow_0.4-4             stats4_4.1.1          
[10] BiocFileCache_2.2.1    utf8_1.2.2             blob_1.2.2            
[13] XML_3.99-0.8           rlang_0.4.12           pillar_1.6.4          
[16] withr_2.4.2            glue_1.5.0             DBI_1.1.1             
[19] rappdirs_0.3.3         BiocGenerics_0.40.0    bit64_4.0.5           
[22] dbplyr_2.1.1           GenomeInfoDbData_1.2.7 foreach_1.5.2         
[25] lifecycle_1.0.1        stringr_1.4.0          zlibbioc_1.40.0       
[28] Biostrings_2.62.0      codetools_0.2-18       memoise_2.0.0         
[31] Biobase_2.54.0         IRanges_2.28.0         fastmap_1.1.0         
[34] doParallel_1.0.17      GenomeInfoDb_1.30.0    curl_4.3.2            
[37] parallel_4.1.1         fansi_0.5.0            AnnotationDbi_1.56.2  
[40] pbmcapply_1.5.1        Rcpp_1.0.8.3           filelock_1.0.2        
[43] cachem_1.0.6           S4Vectors_0.32.2       XVector_0.34.0        
[46] bit_4.0.4              hms_1.1.1              png_0.1-7             
[49] digest_0.6.28          stringi_1.7.5          tools_4.1.1           
[52] bitops_1.0-7           magrittr_2.0.1         tibble_3.1.6          
[55] RCurl_1.98-1.5         RSQLite_2.2.10         crayon_1.4.2          
[58] pkgconfig_2.0.3        ellipsis_0.3.2         xml2_1.3.2            
[61] prettyunits_1.1.1      assertthat_0.2.1       httr_1.4.2            
[64] iterators_1.0.14       R6_2.5.1               compiler_4.1.1

Any idea what's causing this error? Thanks!

xzhoulab / iDEA

EMMCMCStepSummary error #25