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Regarding Error query in publically available RNA seq analysis by R studio

My name is Ruddhida Vidwans, I am a Ph.D. Research Scholar at Jain University, Bengaluru, India. My research area is Forensic Microbiology.

Currently, apart from my Ph.D., I am focusing on learning next-generation sequencing analysis. For that, I am practicing with the publicly available data.

I am using the "GSE163207" ID from GEO datasets for practice.

and referring to the paper entitled "Analysis workflow of publicly available RNA-sequencing datasets" for the analysis guidance".

I am able to perform initial tasks,

But, after rownames(GSE163207)<-clindata$title this command, I got error:

Error in `rownames<-`(`*tmp*`, value = c("Individual 1, PMI 0", "Individual 1, PMI 3",  :
  attempt to set 'rownames' on an object with no dimensions

Can anyone please help me in rectifying this error?

geo rstudio rna-seq ngs
• 1,326 views • link
updated by Ram Ram • written by ruddhida • ruddhida

Welcome Ruddhida. To help other people, please choose a title which describes your problem in a more specific way. Thank you.

It seems as though the object GSE163207 isn't a data.frame, but perhaps a vector. What happens you when you type in class(GSE163207)?

• 0 views • link
written by 4galaxy77 4galaxy77

After

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(c("DESeq2", "GEOquery", "canvasXpress", "ggplot2", "clinfun", "GGally", "factoextra"))

library(DESeq2)
library(GEOquery)
library(canvasXpress)
library(ggplot2)
library(clinfun)
library(GGally)
library(factoextra)

data<-getGEO(GEO = "GSE163207")

head(data)
clindata <- data[["GSE163207_series_matrix.txt.gz"]]@phenoData@data

head(clindata)
head(clindata[,c(1,2,8,40,39,42)])

raw_counts<- read.delim("C:/Users/hp/Documents/GSE163207_series_matrix.txt.gz", stringsAsFactors = FALSE, sep = "")

head(raw_counts) 

raw_counts <- as.matrix(raw_counts)

this command,

I got,

rownames(clindata)<-clindata$title
all(rownames(clindata) %in% colnames(raw_counts))

this as

FALSE instead of TRUE.

• 0 views • link
updated by Ram Ram • written by ruddhida • ruddhida

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