DEG is not filtered.

[chadili]

logFC_t = logFC_cutoff pvalue_t = pvalue_cutoff The above two lines of code did not work. DEG is not filtered.

[tjhwangxiong]

Which function did you refer to?

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--------------原始邮件-------------- 发件人："nitu @.>; 发送时间：2023年12月19日(星期二) 晚上11:05 收件人："tjhwangxiong/TCGAplot" @.>; 抄送："Subscribed @.***>; 主题：[tjhwangxiong/TCGAplot] DEG is not filtered. (Issue #2)

logFC_t = logFC_cutoff pvalue_t = pvalue_cutoff The above two lines of code did not work. DEG is not filtered.

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[chadili]

gene_gsea_go gene_gsea_kegg

[tjhwangxiong]

`gene_gsea_go=function(cancer,gene,logFC_cutoff=2,pvalue_cutoff = 0.05){

exp=subset(tpm,Group=="Tumor" & Cancer==cancer) exp=exp[,-c(1:2)] exp=as.matrix(t(exp))

Group = factor(ifelse(exp[gene,]> median(exp[gene,]),'high','low'),levels=c("low","high")) logFC_t = logFC_cutoff pvalue_t = pvalue_cutoff

DEG

dat=normalizeBetweenArrays(exp) design=model.matrix(~Group) fit=lmFit(dat,design) fit=eBayes(fit) options(digits = 4) DEG=topTable(fit,coef=2,adjust='BH',n=Inf) DEG = na.omit(DEG) DEG$symbol=rownames(DEG)

GSEA

s2e <- clusterProfiler::bitr(DEG$symbol, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db)

DEG <- dplyr::inner_join(DEG,s2e,by=c("symbol"="SYMBOL"))

geneList=DEG$logFC names(geneList)=DEG$ENTREZID geneList=sort(geneList,decreasing = T)

GSEA-GO

Go_gseresult <- clusterProfiler::gseGO(geneList, 'org.Hs.eg.db', keyType = "ENTREZID", ont="BP", pvalueCutoff=1)

transform ENTREZID to gene symbol

Go_gseresult = setReadable(Go_gseresult, OrgDb = "org.Hs.eg.db", keyType = "ENTREZID")

export the GSEA-GO result

write.csv(Go_gseresult@result,file="GSEA_GO.csv",row.names = F)

plot

enrichplot::gseaplot2(Go_gseresult, 1:5, title = cancer)

} ` logFC_t = logFC_cutoff pvalue_t = pvalue_cutoff

We are sorry that "logFC_t" and "pvalue_t" are useless, we will remove them in future. As for GESA-GO and GSEA-KEGG, all genes ranked by logFC have been used as input.