Chuiqin Fan
Chuiqin Fan
Thank you very much for your help!
> @chuiqin Try `install.packages("extrafont")` I'm sorry but I still get the same error after installing packages("extrafont"). `Error in text.default(x, y, labels = labels, col = label.color, family = label.family, :...
> @chuiqin It looks like your R does not support 'Arial' font style when doing plotting. Can you google such issue based on your system of the computer as I...
Thank you! It's so good! ``` # restart your R # upgrade your Matrix package to 1.5.1 install.packages(pkg = "Matrix", force = T) # upgrade GSVA package devtools::install_github("rcastelo/GSVA", force =...
我尝试了1.44.2版本的GSVA，发现它可以正常运行 ``` > library(Seurat) > library(UCell) > library(irGSEA) > packageVersion(pkg = "GSVA") [1] ‘1.44.2’ > pbmc_small 1'. ``` 之后，我通过BiocManager更新GSVA包到1.44.3版本，发现可以重复你的错误 ``` > packageVersion(pkg = "GSVA") [1] ‘1.44.3’ > pbmc_small 1'. ```...
我向GSVA包的作者反馈了这个问题，目前他已经修复了这个错误。 发生错误“no method or default for coercing “matrix” to “dMatrix””的原因是：1周前Matrix包被更新到1.5-0版本。新版本的Matrix包弃用了许多旧函数。这种弃用是不兼容低版本的，因此GSVA包作者更改了代码适应它的变化，但忘记强制指定Matrix包的最低版本。目前作者已经在新版本的GSVA包中强制指定Matrix包的最低版本。 我们可以通过以下代码升级Matrix包和GSVA包的版本： ``` # restart your R # upgrade your Matrix package to 1.5.1 install.packages(pkg = "Matrix", force = T) #...
Can you paste the whole code to make it clearer? Thank you!
错误发生在 scRNA$group ) 这一行代码上。 ***@***.******@***.***>) ***@***.***>中增加了一列全是细胞名称的注释信息。这样，在运行 ***@***.***>里面有一列是细胞类型的注释信息，这一列被命名为celltype，且你想观察不同细胞类型在这4种基因集富集分析方法中共同上调或者共同下调的基因集，可以这样输入： scRNA$group $celltype result.dge 抄送: 范垂钦 ***@***.***>; Mention ***@***.***> 主题: Re: [chuiqin/irGSEA] error in irGSEA step (Issue #3) Hi @chuiqin, Had any idea for...
Can you send me your rds file (scRNA, and the group is inculded in scRNA's metadata, and the AUCell, UCell, singscore, ssgsea score matrix are also inculded in scRNA's assay)...
________________________________ 发件人: Alec hong ***@***.***> 发送时间: 2022年3月17日 11:07 收件人: chuiqin/irGSEA ***@***.***> 抄送: 范垂钦 ***@***.***>; Mention ***@***.***> 主题: Re: [chuiqin/irGSEA] error in irGSEA step (Issue #3) Thanks the reply, But the...