应用R语言处理GEO数据集、ID转化、差异基因分析,在最后一步应用get_deg获取差异基因时报错,提示参数有问题:正常参数输入前几个字母会自动弹出,但报错的参数没有,所以这种情况是还需要进行哪些操作呢,感谢大家帮助
library(WGCNA)
library(tibble)
library(tinyarray)
library(stringr)
library(data.table)
library(AnnoProbe)
library(GEOquery)
library("org.Hs.eg.db")
ost1 <- geo_download("GSE35958")
ost1_exp <-ost1$exp
ost1_pd <-ost1$pd
ost1_exp <-log2(ost1_exp+1)
find_anno("GPL570",install = T)
library(hgu133plus2.db)
ids_570 <- toTable(hgu133plus2SYMBOL)
ost1_exp <-trans_array(ost1_exp,ids_570)
library(stringr)
group <- ifelse(str_detect(ost1_pd$title,"ost"),"ost","con")
group <-as.factor(group)
ids <- as.data.frame(ids_570$symbol)
ids$v2 <- ids_570$symbol
DEGS <- get_deg_all(
ost1_exp,
group,
ids,
entriz = F,
adjust = T,
logFC_cutoff = 2,
pvalue_cutoff = 0.05,
scale.before =FALSE,
n_cutoff = 2,
cluster_cols = TRUE,
annotation_legend = FALSE,
show_rownames = FALSE,
legend=FALSE,
lab = NA,
pkg = 4,
symmetry = FALSE,
my_genes = NULL,
heat.union =TRUE,
heat.id =1,
gene.number=200,
colors_volcano= c("#2874C5", "grey", "#f87669")
)