How could I find Differential Genes in Expression Matrix File NOT gset by R?

Question

[f-tavakoli]

I tried to get gset of my dataset by getGEO function, but unfortunately it didn't work( I installed GEOquery package) and i get errors like this:

Found 1 file(s) GSE69606_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69606/matrix/GSE69606_series_matrix.txt.gz' Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69606/matrix/GSE69606_series_matrix.txt.gz' In addition: Warning message: In download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : InternetOpenUrl failed: ''

So, I decided to work by matrix file.now, i wanna to know how could i get DEGs by R in matrix file, because i don't have LogFC in that file. Thank you all for your help

[f-tavakoli]

Dear Kevin Thank you for your care, i run the commands you suggested, but as i saied before ,i face with errors i left here.

[ATpoint]

Please use ADD REPLY to comment on answers directly. That keeps the thread organized.

[f-tavakoli]

The scripts and their errors i get: series <- "GSE69606"

platform <- "GPL570"

gset <- getGEO(series, GSEMatrix =TRUE, AnnotGPL=TRUE, destdir = "Data/" ) Found 1 file(s) GSE69606_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69606/matrix/GSE69606_series_matrix.txt.gz' Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69606/matrix/GSE69606_series_matrix.txt.gz' In addition: Warning message: In download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : InternetOpenUrl failed: '
' if (length(gset) > 1) idx <- grep(platform, attr(gset, "names")) else idx <- 1 Error: object 'gset' not found gset <- gset[[idx]] Error: object 'gset' not found

[ATpoint]

Hi f-tavakoli,

it could be (and I am just guessing based on previous interactions with users from Iran where you are probably located based on your email address suffix) that NCBI (a governmental US institution) is not accessable from your location due to political sanctioning between the USA and Iran. You might want to try search the web on ways to circumvent this in order to continue your research (VPN).

[f-tavakoli]

Dear ATpoint , i really appreciate your care but it's not about sanctioning because my friends are able to download gset and i tried it using VPN ,too. when i use my colledge's net i receive error i mentioned before and when i use free net i recevie another error including: error in file.exists(destfile): object destfile not found. ( but my set working directory is true!)

anybody know how could i find DEGs using matrix file attached in GEO dataset?

[Devon Ryan]

Hello f-tavakoli!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/9192/how-could-i-find-differential-genes-in-expression-matrix-file-by-r

This is typically not recommended as it runs the risk of annoying people in both communities.

[f-tavakoli]

Hello Devon Thank you for your mention. I didn't know this but I'm in a hurry and nobody replied my question in that site . so, i decided to left my ask here . I apologize.

Answer 1

[Kevin Blighe]

You can obtain the data by running these commands:

library(Biobase)
library(GEOquery)

gset <- getGEO("GSE69606", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

Kevin