Question: GEOquery Problems to Get GEO dataset
4
gravatar for Shicheng Guo
3.4 years ago by
Shicheng Guo7.7k
Shicheng Guo7.7k wrote:

Hi All,

I am applying your great R package GEOquery to get some GEO data. However, I found the exprs function is not working in my case. Can you give me a help. What’s happened here. Thanks.

library("GEOquery")
GSE52271 <- getGEO("GSE52271")
data <- as.data.frame(exprs(GSE52271[[1]]))
phen <- pData(phenoData(GSE52271[[1]]))

After running it, I found ‘data’ is NULL while phen is right. I don’t know why the data is NULL.

Thanks.

OK. Now, It is clear. Thanks @russhh's reply. For NGS dataset, such exp/meth matrix were not provided as the matrix, in which column is sample,row is gene. However, in the last column of the phen files, the exp/meth download links were provided therefore we can download them one by one and then merge them with some way.

geoquery • 1.5k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Shicheng Guo7.7k
4

That s a sequencing expt. I don't think getGEO downloads the data for sequencing experiments, automatically, however, you can use getGEOSuppFiles to download these. HTH

ADD REPLYlink written 3.4 years ago by russhh4.6k
1

>data <- exprs(GSE52271[[1]])

>class(data) [1] "matrix"

>data

 GSM1279516 GSM1279517 GSM1279518 GSM1279519 GSM1279520 GSM1279521
 GSM1279522 GSM1279523 GSM1279524 GSM1279527 GSM1279532

It seems that there are no expression data in first place.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by H.Hasani760
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