Question: Access to analysis to GEO dataset
0
gravatar for Kim
8 months ago by
Kim0
Kim0 wrote:

I need the dataset GSE14098 for my project. I could access the database and analyzed it with GEO2R several times before but now I can only access it, not able to use it with GEO2R anymore. When I check Value Distribution, the message is:

"The requested page has restricted access! https://ibb.co/C6PLwnT

When I choose to display the first 250 results with GEO2R, the message is "Error: Your request could not be completed.​"

I tried to download the Expression set file of GSE14098 to my computer and analyze with R but the program also reports 62 parsing errors so I can't analyze it manually either. I tried with another GEO series and there is no parsing problem

I emailed GEO2R team and they said it still works fine for them.

Does anyone know what happened and how to fix it?

Thank you very much

ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 8 months ago by Kim0
1

I am able to pull up geo2R interface without the restricted access error for GSE14098. Analysis seems to work as well.

ADD REPLYlink modified 8 months ago • written 8 months ago by genomax80k

Hello Genomax. Thank you for checking that and sorry for replying late. I read your answer and tried to figure out my problem before getting back to you. I can also access the dataset and pull up GEO2R interface, the problem just begins with the analysis. I thought it's my connection issue as it works fine for you and the GEO2R and NCBI support teams, so I asked a friend in the US and in Asia to try it (I'm in Germany) and it doesn't work for them either. I really don't know what the problem is. If you could use it normally, could you please help me get the Analysis files? I'll tell you the Group definition and information I need in the result file it is okay for you. Thank you.

ADD REPLYlink written 7 months ago by Kim0

I can use the GEO2R code to download the data:

library(Biobase)
library(GEOquery)

# load series and platform data from GEO

gset <- getGEO("GSE14098", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL571", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

# set parameters and draw the plot

dev.new(width=4+dim(gset)[[2]]/5, height=6)
par(mar=c(2+round(max(nchar(sampleNames(gset)))/2),4,2,1))
title <- paste ("GSE14098", '/', annotation(gset), " selected samples", sep ='')
boxplot(exprs(gset), boxwex=0.7, notch=T, main=title, outline=FALSE, las=2)
ADD REPLYlink written 6 months ago by Kevin Blighe56k
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