Question: How could I find Differential Genes in Expression Matrix File NOT gset by R?
1
gravatar for f-tavakoli
7 days ago by
f-tavakoli10
f-tavakoli10 wrote:

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

deg microarray bioconductor R • 137 views
ADD COMMENTlink modified 6 days ago by zx87547.9k • written 7 days ago by f-tavakoli10

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.

ADD REPLYlink written 6 days ago by f-tavakoli10

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

ADD REPLYlink written 6 days ago by ATpoint21k

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

ADD REPLYlink written 6 days ago by f-tavakoli10

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).

ADD REPLYlink modified 6 days ago • written 6 days ago by ATpoint21k

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?

ADD REPLYlink written 6 days ago by f-tavakoli10

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.

ADD REPLYlink written 6 days ago by Devon Ryan91k

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.

ADD REPLYlink written 6 days ago by f-tavakoli10
0
gravatar for Kevin Blighe
7 days ago by
Kevin Blighe46k
Kevin Blighe46k wrote:

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

ADD COMMENTlink written 7 days ago by Kevin Blighe46k
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