Error while running survival analysis ?

I'm interested in plotting KM survival curve for genes based on median bifuraction of low and high expression groups. However, while running I;m getting an error stating that:

"Error in names(.cols) <- grp.levels : 
  'names' attribute [385] must be the same length as the vector [381]"

My Code is as follows:

library(survival)
library(survminer)
library(dplyr)
library(survMisc)
library(GGally)
library(survcomp)
library(RegParallel)



JMS <- read.delim(file = "SURVIVAL_47.txt")
JMS = JMS %>% mutate(group = case_when(AURKA > quantile(AURKA, 0.5) ~ 'AURKA(High)', AURKA < quantile(AURKA, 0.5) ~ 'AURKA(Low)', TRUE ~ NA_character_ ))

fit <- survfit(Surv(Time, Status) ~ AURKA, data = JMS)

ggsurvplot(fit, pval = TRUE, conf.int = TRUE, risk.table = TRUE, risk.table.y.text.col = TRUE)

My data (SURVIVAL_47.txt") is available at:

SURVIVAL_47.txt:

km os plot rna-seq

• 1,489 views • link

updated 3.5 years ago by bkleiboeker •

• written 3.5 years ago by prithvi.mastermind •

Which line specifically is giving you this error?

The error seems fairly self explanatory: one of these functions is trying to assign column names as grp.levels (likely an internal variable), but the two objects are different lengths. In my experience there's a good chance this error stems from something simple like empty rows/columns in your starting .txt file, ambiguous group names, passing extra sample name/condition/group info columns to a function which is intended to only take a matrix of values, etc.

• 0 views • link

written 3.5 years ago by bkleiboeker •

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