error in irGSEA step

[honghh2018]

Hi developer, Thanks develop the great tools. The error showing up when running the irGSEA, the error lying below: Registered S3 method overwritten by 'spatstat.geom': method from print.boxx cli Attaching SeuratObject Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Validating object structure Updating object slots Ensuring keys are in the proper strucutre Ensuring feature names don't have underscores or pipes Object representation is consistent with the most current Seurat version Calculate AUCell scores Finish calculate AUCell scores Calculate UCell scores Finish calculate UCell scores Calculate singscore scores Finish calculate singscore scores Calculate ssgsea scores Finish calculate ssgsea scores Calculate differential gene set : AUCell Calculate differential gene set : UCell Calculate differential gene set : singscore Calculate differential gene set : ssgsea Mutate "has no methods that apply to the target object of "list" Calls: irGSEA.integrate -> %>% ->

R.version _
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 1.2
year 2021
month 11
day 01
svn rev 81115
language R
version.string R version 4.1.2 (2021-11-01) nickname Bird Hippie

Had any idea for this issue? Best, hanhuihong

[chuiqin]

Can you paste the whole code to make it clearer? Thank you!

[honghh2018]

Hi chuiqin,

The while code lying below: scRNA<-CreateSeuratObject(df2,project = 'bulk') scRNA<-NormalizeData(scRNA) scRNA <- irGSEA.score(object = scRNA, assay = "RNA",slot = "data", seeds = 123, ncores = 1,min.cells = 3, min.feature = 0, subcategory = NULL, geneid = "symbol",method = c("AUCell", "UCell", "singscore","ssgsea"), aucell.MaxRank = NULL, ucell.MaxRank = NULL,kcdf = 'Gaussian',custom = T,geneset = aa)

scRNA$group<-rownames(scRNA@meta.data)

result.dge <- irGSEA.integrate(object = scRNA,metadata = NULL,group.by = 'group', col.name = NULL,method = c("AUCell","UCell","singscore","ssgsea"))

save(result.dge,scRNA,file = "allresult.rda")

R.version _
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 0.2
year 2020
month 06
day 22
svn rev 78730
language R
version.string R version 4.0.2 (2020-06-22) nickname Taking Off Again

Best hanhuihong

[honghh2018]

Hi @chuiqin, Had any idea for this issue?

Best, hanhuihong

[chuiqin]

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 <- irGSEA.integrate(object = scRNA,metadata = NULL,group.by = 'group', col.name = NULL,method = c("AUCell","UCell","singscore","ssgsea")

又或者直接可以这样输入： result.dge <- irGSEA.integrate(object = scRNA,metadata = NULL,group.by = 'celltype', col.name = NULL,method = c("AUCell","UCell","singscore","ssgsea")

---

发件人: Alec hong @.> 发送时间: 2022年3月16日 20:25 收件人: chuiqin/irGSEA @.> 抄送: 范垂钦 @.>; Mention @.> 主题: Re: [chuiqin/irGSEA] error in irGSEA step (Issue #3)

Hi @chuiqinhttps://github.com/chuiqin, Had any idea for this issue?

Best, hanhuihong

― Reply to this email directly, view it on GitHubhttps://github.com/chuiqin/irGSEA/issues/3#issuecomment-1069070993, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APWKDPDD37D34P6D5TDQ42TVAHHJ5ANCNFSM5QOJUD4A. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.***>

[honghh2018]

Hi @chuiqin I get the group into the seurat object,like below:

anno[-c(86:90)] [1] "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" [20] "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" [39] "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" [58] "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" [77] "B" "C" "A" "B" "C" "A" "B" "C" "A" But it still get error:

anno[-c(86:90)] [1] "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" [20] "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" [39] "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" [58] "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" [77] "B" "C" "A" "B" "C" "A" "B" "C" "A" anno=anno[-c(86:90)] scRNA$group<-anno result.dge <- irGSEA.integrate(object = scRNA,metadata = NULL,group.by = 'group', col.name = NULL,method = cCalculate differential gene set : AUCell Calculate differential gene set : UCell Calculate differential gene set : singscore Calculate differential gene set : ssgsea Error in UseMethod("mutate") : "mutate"没有适用于"list"目标对象的方法

It seem like the mutate function can not be work well.

Best, Hanhuihong

[chuiqin]

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) to my email @.***)? I want to test whether the problem comes from the rds file.

---

发件人: Alec hong @.> 发送时间: 2022年3月17日 9:48 收件人: chuiqin/irGSEA @.> 抄送: 范垂钦 @.>; Mention @.> 主题: Re: [chuiqin/irGSEA] error in irGSEA step (Issue #3)

Hi @chuiqinhttps://github.com/chuiqin I get the group into the seurat object,like below:

anno[-c(86:90)] [1] "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" [20] "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" [39] "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" [58] "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" [77] "B" "C" "A" "B" "C" "A" "B" "C" "A" But it still get error:

anno[-c(86:90)] [1] "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" [20] "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" [39] "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" [58] "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" "B" "C" "A" [77] "B" "C" "A" "B" "C" "A" "B" "C" "A" anno=anno[-c(86:90)] scRNA$group<-anno result.dge <- irGSEA.integrate(object = scRNA,metadata = NULL,group.by = 'group', col.name = NULL,method = cCalculate differential gene set : AUCell Calculate differential gene set : UCell Calculate differential gene set : singscore Calculate differential gene set : ssgsea Error in UseMethod("mutate") : "mutate"没有适用于"list"目标对象的方法

It seem like the mutate function can not be work well.

Best, Hanhuihong

― Reply to this email directly, view it on GitHubhttps://github.com/chuiqin/irGSEA/issues/3#issuecomment-1069823130, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APWKDPEXZU6T4HZJXADF5Y3VAKFOHANCNFSM5QOJUD4A. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.***>

[honghh2018]

Thanks the reply, But the email is weird, it showing me asterisk like below picture What happen for this?

[chuiqin]

---

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 email is weird, it showing me asterisk like below picture [image]https://user-images.githubusercontent.com/41668708/158728593-ec2cb464-8df7-4219-ad91-e7a7008b7d15.png What happen for this?

― Reply to this email directly, view it on GitHubhttps://github.com/chuiqin/irGSEA/issues/3#issuecomment-1070073475, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APWKDPGU2BP2FZFQCSD62ZLVAKOWPANCNFSM5QOJUD4A. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.***>

[honghh2018]

Hi @chuiqin ， The seurat object generated by 85 samples from bulk sequencing. i convert it into seurat and using it to analysis the genes score. The email site can not be recognized by the asterisk. Hope can sent me the real email site. Best, Hanhuihong

[chuiqin]

Can you upload your rds file to Baidu Netdisk？

Get Outlook for Androidhttps://aka.ms/AAb9ysg

---

From: Alec hong @.> Sent: Friday, March 18, 2022 2:25:13 PM To: chuiqin/irGSEA @.> Cc: 范垂钦 @.>; Mention @.> Subject: Re: [chuiqin/irGSEA] error in irGSEA step (Issue #3)

Hi @chuiqinhttps://github.com/chuiqin ， The seurat object generated by 85 samples from bulk sequencing. i convert it into seurat and using it to analysis the genes score. The email site can not be recognized by the asterisk. Hope can sent me the real email site. Best, Hanhuihong

― Reply to this email directly, view it on GitHubhttps://github.com/chuiqin/irGSEA/issues/3#issuecomment-1072069945, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APWKDPFHVH4APH64GJMC2ETVAQOUTANCNFSM5QOJUD4A. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.***>

[chuiqin]

请问问题解决了吗？如果不介意的话，你是否可以把(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)打包成一个rds文件，通过百度云链接传递给我？又或者可以加我微信号fcq065837，让我可以测试一下是数据文件问题，还是R包代码问题。Github屏蔽了我的邮件地址，我每次在回复中发邮件地址都会是星号。

[huangtao334]

Calculate differential gene set : AUCell Calculate differential gene set : UCell Calculate differential gene set : singscore Calculate differential gene set : ssgsea Error in UseMethod("mutate") : "mutate"没有适用于"list"目标对象的方法 ,类似问题，解决了么

[chuiqin]

Calculate differential gene set : AUCell Calculate differential gene set : UCell Calculate differential gene set : singscore Calculate differential gene set : ssgsea Error in UseMethod("mutate") : "mutate"没有适用于"list"目标对象的方法 ,类似问题，解决了么

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。