How to download matrix of the "GSE73554"

Question

[adR]

Hello,

First of all, Thank you for your time and help!

Could please give me some directions on how to download publicly available RNAseq data "GSE73554" I used command lines:

KO_RF_GSE73554 <- download.file("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi", "GSE73554_KO_RF_Intron_Exon_RFP.txt.gz")
KO_RF_GSE73554 <- read.csv("GSE73554_KO_RF_Intron_Exon_RFP.txt.gz", sep="\t")
Data <- read.table(gzfile("GSE73554_KO_RF_Intron_Exon_RFP.txt.gz"),sep="\t")

I also tried the following command lines:

library(Biobase)
library(GEOquery)
gset <- getGEO("GSE73554", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL17021", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]
da <- gset@phenoData@data

However, both attempts could not help me to get the matrix of the expression. Therefore, I may ask for some tips, please?

Thank you!
AD

[jared.andrews07]

I have changed this to a "Question" as the "Tutorial" flag is for actual tutorials. Additionally, please use the code formatting button (the one with 1s and 0s) when appropriate, as it makes the code much easier to follow. I have done it for you this time.

Lastly, you say your code isn't working. How isn't it working? Do you get an error? Is the format not what you want, and if so, how? What do you expect/need?

[adR]

Hi Andrews, Thank you! Actually didn't get an error in my code and in your codes as well. What I am looking for in this "GSE73554" is the expression profile (the matrix of the expression profile like the list of genes in the rows and samples in the columns). Thanks!

Answer 1

[MatthewP]

# continute your code
# Expression matrix
exprData <- exprs(gset)
# phenotype data
phenoData <- pData(gset)

[adR]

Hi Matthew, Thank you for your answer. Actually didn't get an error in my code and in your codes as well. What I am looking for in this "GSE73554" is the expression profile (the matrix of the expression profile like the list of genes in the rows and samples in the columns). Thanks!