HI,

I'm getting following warning from nullp function from goseq package.

pwf=nullp(gene.vector1, bias.data=length.vec)
Komunikat ostrzegawczy:
W poleceniu 'pcls(G)': initial point very close to some inequality constraints

I've read here goseq: In pcls(G) : initial point very close to some inequality constraints that it is okay if the plot looks reasonably. In my case it is not,

I'm working on maize so I have to prepare input files manually, here is a summary of the files

> gene.vector1[1:5]
Zm00001eb015280 Zm00001eb000610 Zm00001eb033210 Zm00001eb044610 Zm00001eb014360 
              0               0               0               0               0 
> length.vec[1:5]
[1] 1624  385  990 1182  386
> length(gene.vector1)
[1] 44303
> length(length.vec)
[1] 44303

I have 746 DE genes.

Should I be concerned with such result?

Here is my setup

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

time zone: Europe/Warsaw
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] rtracklayer_1.60.0     GenomicRanges_1.52.0   GenomeInfoDb_1.36.1   
[4] IRanges_2.34.1         S4Vectors_0.38.1       BiocGenerics_0.46.0   
[7] goseq_1.52.0           geneLenDataBase_1.36.0 BiasedUrn_2.0.10      

loaded via a namespace (and not attached):
 [1] KEGGREST_1.40.0             SummarizedExperiment_1.30.2
 [3] rjson_0.2.21                Biobase_2.60.0             
 [5] lattice_0.22-5              vctrs_0.6.5                
 [7] tools_4.3.2                 bitops_1.0-7               
 [9] generics_0.1.3              curl_5.0.1                 
[11] parallel_4.3.2              tibble_3.2.1               
[13] fansi_1.0.6                 AnnotationDbi_1.62.2       
[15] RSQLite_2.3.1               blob_1.2.4                 
[17] pkgconfig_2.0.3             Matrix_1.6-5               
[19] dbplyr_2.3.3                lifecycle_1.0.4            
[21] GenomeInfoDbData_1.2.10     compiler_4.3.2             
[23] stringr_1.5.0               Rsamtools_2.16.0           
[25] Biostrings_2.68.1           progress_1.2.2             
[27] codetools_0.2-19            RCurl_1.98-1.12            
[29] yaml_2.3.7                  GO.db_3.17.0               
[31] pillar_1.9.0                crayon_1.5.2               
[33] BiocParallel_1.34.2         DelayedArray_0.26.6        
[35] cachem_1.0.8                nlme_3.1-163               
[37] tidyselect_1.2.0            digest_0.6.34              
[39] stringi_1.7.12              dplyr_1.1.2                
[41] restfulr_0.0.15             splines_4.3.2              
[43] biomaRt_2.56.1              fastmap_1.1.1              
[45] grid_4.3.2                  cli_3.6.2                  
[47] magrittr_2.0.3              S4Arrays_1.0.4             
[49] GenomicFeatures_1.52.1      utf8_1.2.4                 
[51] XML_3.99-0.14               rappdirs_0.3.3             
[53] filelock_1.0.2              prettyunits_1.1.1          
[55] bit64_4.0.5                 XVector_0.40.0             
[57] httr_1.4.6                  matrixStats_1.0.0          
[59] bit_4.0.5                   png_0.1-8                  
[61] hms_1.1.3                   memoise_2.0.1              
[63] BiocIO_1.10.0               BiocFileCache_2.8.0        
[65] mgcv_1.9-1                  rlang_1.1.3                
[67] glue_1.7.0                  DBI_1.1.3                  
[69] xml2_1.3.5                  R6_2.5.1                   
[71] MatrixGenerics_1.12.2       GenomicAlignments_1.36.0   
[73] zlibbioc_1.46.0

The plot looks a good as is possible given the data. It appears that goseq is working correctly and the warning can be ignored.