Chuiqin Fan

In irGESA, some gene set scoring methods, such as AUCell, UCell, singscore, ssgsea, JASMINE and viper, work based on the expression rank of individual cells. These scoring methods are batch...

我很抱歉现在才回复你。之前在手机邮箱上直接回复issue，但直到今天登录网页才发现这个回复信息并没有出现在issue里面。请问你现在的问题解决了吗？

方便打印一下c5gsbp这个变量前几个的信息吗？我观察一下是否是格式出来问题。

我使用pbmc示例数据运行了你的代码，发现是可以正常运行的。 ``` library(irGSEA) library(GSVA) library(GSEABase) library(clusterProfiler) c5gsbp

Yes, this is a bug. I fixed this BUG in the new version of irGSEA. This bug can be fixed by uninstalling the old version of irGSEA and installing the...

首先，检查一下是否有`celltype`这一列存在，以及随机挑选一个Assay验证一下是否存在，可以这样操作： ``` unique(Neutrophi_rename.final2$celltype) Neutrophi_rename.final2[["AUCell"]]@scale.data[1:2,1:2] ``` 如果存在，随机挑一个Assay检查一下这些基因集是否真的在这些细胞类型中存在差异； ``` Idents(Neutrophi_rename.final2)

还可以排除一下Seurat的版本。错误的发生是因为Seurat从5.02开始，增加了一个fc.slot参数。如果你要计算`scale.data`的差异，不管是`FindAllMarkers`还是`FindMarkers`函数，没有指定`fc.slot`，计算的时候都会出错。恰好irGSEA的打分矩阵都存放在scale.data里面。我在新版本的irGSEA（version 3.2.4）里面已经修复了这个错误，只要重新安装irGSEA即可解决这个问题。 

First, packages 'AUCell', 'ComplexHeatmap', 'decoupleR', 'ggtree', 'Nebulosa', 'singscore' are not available in CRAN. Please consider to install them from Bioconductor as follow: ``` # install packages from Bioconductor bioconductor.packages

> Please help me to solve this error, Warning in install.packages : packages ‘UCell’, ‘irGSEA’ are not available for this version of R > > Versions of these packages for...

The occurrence of this error is confusing, can you post your complete process, Seurat version and irGSEA version? Just like the following code: ``` library(Seurat) library(SeuratData) library(RcppML) library(irGSEA) data("pbmc3k.final") pbmc3k.final