Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error when calculate irGSEA.score using category = "C5", subcategory = "GO:BP" parameter #18

Open
itolov opened this issue Nov 3, 2022 · 1 comment

Comments

@itolov
Copy link

itolov commented Nov 3, 2022

hi developer, thank you so much for your helpful tools.
I tried to use irGSEA to calculate the GO -BP geneset enrichment scores. But when I calculated the enrichment score as shown below:
skin.GO.BP <- irGSEA.score(object = skin.combined, assay = "RNA", slot = "data", seeds = 123, ncores = 1, min.cells = 3, min.feature = 0, custom = F, geneset = NULL, msigdb = T, species = "Mus musculus", category = "C5", subcategory = "GO:BP", geneid = "symbol", method = c("AUCell", "UCell", "singscore", "ssgsea"), aucell.MaxRank = NULL, ucell.MaxRank = NULL, kcdf = 'Gaussian')
the reaction was:

Error in calculate_Uscore(m, features = features, maxRank = maxRank, chunk.size = chunk.size, : One or more signatures contain more genes than maxRank parameter.
Increase maxRank parameter or make shorter signatures
Traceback:

  1. irGSEA.score(object = skin.combined, assay = "RNA", slot = "data",
    . seeds = 123, ncores = 1, min.cells = 3, min.feature = 0,
    . custom = F, geneset = NULL, msigdb = T, species = "Mus musculus",
    . category = "C5", subcategory = "BP", geneid = "symbol", method = c("AUCell",
    . "UCell", "singscore", "ssgsea"), aucell.MaxRank = NULL,
    . ucell.MaxRank = NULL, kcdf = "Gaussian")
  2. UCell::ScoreSignatures_UCell(matrix = my.matrix, features = h.gsets.list,
    . maxRank = ucell.MaxRank, w_neg = 1, ncores = ncores, force.gc = T)
  3. calculate_Uscore(m, features = features, maxRank = maxRank, chunk.size = chunk.size,
    . w_neg = w_neg, ties.method = ties.method, ncores = ncores,
    . BPPARAM = BPPARAM, force.gc = force.gc, name = name)
  4. stop("One or more signatures contain more genes than maxRank parameter.\n Increase maxRank parameter or make shorter signatures")

I am confused because I used a similar code to get the hallmark and KEGG results.
Could you give me any suggestions?
Or does anyone have an idea as to why this occurs?

@itolov itolov changed the title Error when calculate irGSEA.score using category = "C5", subcategory = "BP" parameter Error when calculate irGSEA.score using category = "C5", subcategory = "GO:BP" parameter Nov 4, 2022
@sherryshen2020
Copy link

ucell.MaxRank Maximum number of genes to rank per cell. Above this rank, a given gene is considered as not expressed. Default 1500 when it set to NULL. You can input special number, such as 2000, to increase the rank range. The parameter works if "UCell" is selected in "method".

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants