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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Please use "options(scipen = 100)" before running infercnv if you are using the analysis_mode="subclusters" #573

Open stroke1989 opened 1 year ago

stroke1989 commented 1 year ago

Hi, Thanks for this good tool, I sucessfully installed infercnv, while I test the example data, error ocurred:

library(infercnv) The legacy packages maptools, rgdal, and rgeos, underpinning the sp package, which was just loaded, will retire in October 2023. Please refer to R-spatial evolution reports for details, especially https://r-spatial.org/r/2023/05/15/evolution4.html. It may be desirable to make the sf package available; package maintainers should consider adding sf to Suggests:. The sp package is now running under evolution status 2 (status 2 uses the sf package in place of rgdal) infercnv_obj = CreateInfercnvObject(raw_counts_matrix=system.file("extdata", "oligodendroglioma_expression_downsampled.counts.matrix.gz", package = "infercnv"), annotations_file=system.file("extdata", "oligodendroglioma_annotations_downsampled.txt", package = "infercnv"), delim="\t", gene_order_file=system.file("extdata", "gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt", package = "infercnv"),ref_group_names=c("Microglia/Macrophage","Oligodendrocytes (non-malignant)"))

INFO [2023-07-13 12:54:43] Parsing matrix: /home/neurospine/R/x86_64-pc-linux-gnu-library/4.3/infercnv/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz INFO [2023-07-13 12:54:44] Parsing gene order file: /home/neurospine/R/x86_64-pc-linux-gnu-library/4.3/infercnv/extdata/gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt INFO [2023-07-13 12:54:44] Parsing cell annotations file: /home/neurospine/R/x86_64-pc-linux-gnu-library/4.3/infercnv/extdata/oligodendroglioma_annotations_downsampled.txt INFO [2023-07-13 12:54:44] ::order_reduce:Start. INFO [2023-07-13 12:54:44] .order_reduce(): expr and order match. INFO [2023-07-13 12:54:45] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10338,184 Total=18322440.6799817 Min=0 Max=34215. INFO [2023-07-13 12:54:45] num genes removed taking into account provided gene ordering list: 399 = 3.8595473012188% removed. INFO [2023-07-13 12:54:45] -filtering out cells < 100 or > Inf, removing 0 % of cells WARN [2023-07-13 12:54:45] Please use "options(scipen = 100)" before running infercnv if you are using the analysis_mode="subclusters" option or you may encounter an error while the hclust is being generated. INFO [2023-07-13 12:54:45] validating infercnv_obj

I'm not a bioinformatic analyst，could anyone help me out? Appreciate!

rpeys commented 1 year ago

That looks just like a warning, not an error, to me. Setting options(scipen = 100) just means that R should print full numbers, instead of numbers in scientific notation, unless they are more than 100 digits long. You can literally just run that code options(scipen = 100) before running the infercnv command and the warning should go away