Hello, I am dealing with an error I could not yet solve. I am comparing different ranked gene lists with RobustRankedAgrreg package in R.
With the short lists of sign. DGE the creation of a rankMatrix worked fine.
> str(gene_list_ordered)
List of 6 $ DEGs_193677_LFC1_p0.01: chr [1:114] "NPSR1"... $ DEGs_13367_LFC1_p0.01 : chr [1:18] "CXCL13" ... $ DEGs_38713_LFC1_p0.01 : chr [1:593] "AQP8"... $ DEGs_59071_LFC1_p0.01 : chr [1:149] "SLC6A14" ... $ DEGs_73661_LFC1_p0.01 : chr [1:163] "SLC6A14" ... $ DEGs_16879_LFC1_p0.01 : chr [1:74] "DEFA5" .....
> rankmat<- RobustRankAggreg::rankMatrix(glist = gene_list_ordered, N=c(114, 18, 593, 149, 163, 74), full = TRUE)
But when I tried to feed the actual, large gene lists in the rankMatrix function, there seemed to be a problem with the length of the first gene list. I already tried to limit the number of genes, chopped the gene lists to the same length and went into the error-debugging but I could not solve the problem.
> str(gene_list_ordered2)
List of 6 $ DEGs_193677: chr [1:36584] "NPSR1" "MTND1P23" "RPL7P31" "LINC01819" ... $ DEGs_13367 : chr [1:23519] "CXCL13" "DEFA5" "AQP8" "PSPH" ... $ DEGs_38713 : chr [1:22990] "AQP8" "SLC51A" "ABCG2" "MMP1" ... $ DEGs_59071 : chr [1:23279] "SLC6A14" "MEP1B" "SLC38A4" "AQP8" ... $ DEGs_73661 : chr [1:23209] "SLC6A14" "DEFA5" "EGR1" "FOS" ... $ DEGs_16879 : chr [1:23521] "DEFA5" "SLC6A14" "AQP8" "DEFA6" ...
> count
[1] 36584 23519 22990 232279 23209 23521
> rankmat<- RobustRankAggreg::rankMatrix(glist = gene_list_ordered2, N= count, full = FALSE)
Error in [<-(*tmp*, glist[[i]], i, value = (1:length(glist[[i]]))/N[i]) :
subscript out of bounds
My session info:
R version 4.3.3 Patched (2024-02-29 r86188)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] RobustRankAggreg_1.2.1
