Question: How to download matrix of the "GSE73554"
0
gravatar for Do it!
5 weeks ago by
Do it!10
Do it!10 wrote:

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

rna-seq tutorial • 111 views
ADD COMMENTlink modified 5 weeks ago by MatthewP690 • written 5 weeks ago by Do it!10

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?

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by jared.andrews076.4k

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!

ADD REPLYlink written 5 weeks ago by Do it!10
1
gravatar for MatthewP
5 weeks ago by
MatthewP690
China
MatthewP690 wrote:
# continute your code
# Expression matrix
exprData <- exprs(gset)
# phenotype data
phenoData <- pData(gset)
ADD COMMENTlink written 5 weeks ago by MatthewP690

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!

ADD REPLYlink written 5 weeks ago by Do it!10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1867 users visited in the last hour