genes not being identical between reference and my gene expression data

[MjelleLab]

I am having problems with genes not being identical between reference and my gene expression data. Any idea?

set_cibersort_binary("~/CIBERSORT/CIBERSORT.R")
set_cibersort_mat("~/CIBERSORT/LM22.txt")
immunedeconv.out.cibersort <- immunedeconv::deconvolute(top.names.out, "cibersort")

>>> Running cibersort
 Error in (function (sig_matrix = lm22, mixture_file, perm, QN = TRUE, : 
None identical gene between eset and reference had been found.
Check your eset using: intersect(rownames(eset), rownames(reference))

> top.names.out[1:4,1:4]
       sample1.isf.gene_data sample2.isf.gene_data  sample3.isf.gene_data sample4.isf.gene_data
TSPAN6                       1.639                     4.37300                   9.691e-01                      1.6140
TNMD                         0.000                     0.02749                   1.519e-07                      0.0000
DPM1                         1.662                     5.28300                   2.166e+00                      0.9807
SCYL3                        2.412                     1.31400                   9.759e-01                      1.7750
```

[grst]

Your top.names.out looks alright. Have you tried checking manually if there is any overlap?

Something like

lm22 = readr::read_tsv("LM22.txt")
intersect(lm22$`Gene symbol`, rownames(top.names.out))

[wlei-amu]

Hi，I check my lm22.txt and exp_tpm,
intersect(lm22$Gene symbol, rownames(top.names.out))
it has 522 genes overlap,but I also have this error.
Thanks!

[sur-yang]

I have the same issue. Have you solved the question?

[sagarutturkar]

Any updates on this issue would be helpful.

[rhea977]

same issue. any updates?

[grst]

I would like to investigate that further...

Could you please post

• your sessionInfo() after the error occurs and
• the version of the CIBERSORT.R script (should be the first line, mine is # CIBERSORT R script v1.04 (last updated 10-24-2016))

[sagarutturkar]

Attached is the LM22 signature file. LM22.txt
Script version - # CIBERSORT R script v1.04 (last updated 10-24-2016)
SessionInfo - sessionInfo():

[LM22.txt](https://github.com/omnideconv/immunedeconv/files/10817257/LM22.txt)

> sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

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

other attached packages:
 [1] immunedeconv_2.1.0 EPIC_1.1.5         data.table_1.14.6  kableExtra_1.3.4   knitr_1.42         forcats_1.0.0     
 [7] stringr_1.5.0      purrr_1.0.1        readr_2.1.4        tidyr_1.3.0        tibble_3.1.8       ggplot2_3.4.1     
[13] tidyverse_1.3.2    dplyr_1.1.0       

loaded via a namespace (and not attached):
  [1] googledrive_2.0.0      colorspace_2.1-0       ellipsis_0.3.2         XVector_0.38.0         fs_1.6.1              
  [6] rstudioapi_0.14        ComICS_1.0.4           bit64_4.0.5            AnnotationDbi_1.60.0   fansi_1.0.4           
 [11] lubridate_1.9.2        xml2_1.3.3             codetools_0.2-19       splines_4.2.0          cachem_1.0.6          
 [16] jsonlite_1.8.4         broom_1.0.3            annotate_1.76.0        dbplyr_2.3.0           png_0.1-8             
 [21] pheatmap_1.0.12        data.tree_1.0.0        compiler_4.2.0         httr_1.4.4             backports_1.4.1       
 [26] assertthat_0.2.1       Matrix_1.5-3           fastmap_1.1.0          limma_3.54.1           gargle_1.3.0          
 [31] cli_3.6.0              prettyunits_1.1.1      htmltools_0.5.4        tools_4.2.0            gtable_0.3.1          
 [36] glue_1.6.2             GenomeInfoDbData_1.2.9 rappdirs_0.3.3         Rcpp_1.0.10            Biobase_2.58.0        
 [41] cellranger_1.1.0       vctrs_0.5.2            Biostrings_2.66.0      preprocessCore_1.60.2  nlme_3.1-162          
 [46] svglite_2.1.1          xfun_0.37              openxlsx_4.2.5.2       rvest_1.0.3            timechange_0.2.0      
 [51] lifecycle_1.0.3        XML_3.99-0.13          googlesheets4_1.0.1    edgeR_3.40.2           MASS_7.3-58.2         
 [56] zlibbioc_1.44.0        scales_1.2.1           vroom_1.6.1            hms_1.1.2              parallel_4.2.0        
 [61] RColorBrewer_1.1-3     curl_5.0.0             yaml_2.3.7             memoise_2.0.1          biomaRt_2.52.0        
 [66] stringi_1.7.12         RSQLite_2.2.20         highr_0.10             genefilter_1.78.0      S4Vectors_0.36.1      
 [71] filelock_1.0.2         BiocGenerics_0.44.0    testit_0.13            zip_2.2.2              BiocParallel_1.32.5   
 [76] GenomeInfoDb_1.34.9    rlang_1.0.6            pkgconfig_2.0.3        systemfonts_1.0.4      bitops_1.0-7          
 [81] matrixStats_0.63.0     evaluate_0.20          lattice_0.20-45        cowplot_1.1.1          bit_4.0.5             
 [86] tidyselect_1.2.0       magrittr_2.0.3         R6_2.5.1               IRanges_2.32.0         generics_0.1.3        
 [91] DBI_1.1.3              pillar_1.8.1           haven_2.5.1            withr_2.5.0            mgcv_1.8-41           
 [96] survival_3.5-0         KEGGREST_1.38.0        RCurl_1.98-1.10        modelr_0.1.10          crayon_1.5.2          
[101] utf8_1.2.3             BiocFileCache_2.4.0    tzdb_0.3.0             rmarkdown_2.20         mMCPcounter_1.1.0     
[106] progress_1.2.2         locfit_1.5-9.7         grid_4.2.0             readxl_1.4.2           sva_3.46.0            
[111] blob_1.2.3             reprex_2.0.2           digest_0.6.31          webshot_0.5.4          xtable_1.8-4          
[116] stats4_4.2.0           munsell_0.5.0          viridisLite_0.4.1     

Error and warnings:

>>> Running cibersort
Error in (function (sig_matrix = lm22, mixture_file, perm, QN = TRUE,  : 
  None identical gene between eset and reference had been found.
         Check your eset using: intersect(rownames(eset), rownames(reference))
In addition: Warning message:
The `path` argument of `write_tsv()` is deprecated as of readr 1.4.0.
ℹ Please use the `file` argument instead.
ℹ The deprecated feature was likely used in the immunedeconv package.
  Please report the issue at <https://github.com/omnideconv/immunedeconv/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

[grst]

Hi @sagarutturkar, I don't manage to reproduce this error with my datasets.
Is there any chance you could send me your dataset (or a subset of it that still produces the error)? If the data cannot be shared publicly, you can reach out to me via email (see my github profile for contact details).

[sagarutturkar]

I am using the data provided with package.

library(immunedeconv)

cibersort_binary = "C/immunedeconv_test/CIBERSORT.R"
cibersort_mat = "C/immunedeconv_test/LM22.txt"

res_cibersort <- deconvolute(dataset_racle$expr_mat, "cibersort", tumor = TRUE)

[grst]

That's amazing :/ The example dataset works without issues for me with pretty much the same package versions as you indicated above. I still need to try this on Windows if I get a chance.

Btw, does this only affect cibersort, or also other deconvolution methods?

[sagarutturkar]

oh! I will try to install this package on Linux servers.

This only affects ciberosort. I am able to run the rest quantiseq, epic, mcp_counter without any error.

[LorenzoMerotto]

@grst I have tested it on Windows and for me it works, I have the same version (2.1.0)

However I highly doubt that we're not using the same Cibersort script.
This error message

Error in (function (sig_matrix = lm22, mixture_file, perm, QN = TRUE, : None identical gene between eset and reference had been found. Check your eset using: intersect(rownames(eset), rownames(reference))

Is not coded in immunedeconv and is not on my CIBERSORT script either

[grst]

That's a good hint! Maybe the cibersort script got updated, but they didn't bump the version number.

@sagarutturkar, could you please send me and/or Lorenzo your Cibersort version by email?

[sagarutturkar]

@grst sent you the script by email. Thank you for the help.

[grst]

Hi all,

the reason of this error is the use of an unofficial version of the CIBERSORT.R script (most likely downloaded from https://github.com/IOBR/IOBR/blob/905127ffa32aee5e1fa6c305c2e14e7c918a5967/R/CIBERSORT.R), which has been modified.

Only the version downloaded from the official CIBERSORT website is compatible with immunedeconv.