Question: Access to analysis to GEO dataset
0
gravatar for Kim
12 months ago by
Kim10
Kim10 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 11 months ago by Biostar ♦♦ 20 • written 12 months ago by Kim10
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 12 months ago • written 12 months ago by genomax87k

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 11 months ago by Kim10

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 10 months ago by Kevin Blighe63k
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