0

I am trying to analyze a gene expression dataset GSE113590, but I am getting Null expr values. 

source("http://bioconductor.org/biocLite.R")
biocLite("GEOquery")
library(GEOquery)


gset <- getGEO("GSE113590", GSEMatrix =TRUE)
if (length(gset) > 1) idx <- grep("GPL20301", attr(gset, "names")) else idx <- 1
 gset <- gset[[idx]]

> str(exprs(gset))

 logi[0 , 1:32] 
 - attr(*, "dimnames")=List of 2
  ..$ : NULL
  ..$ : chr [1:32] "GSM3109311" "GSM3109312" "GSM3109313" "GSM3109314" ...

In my practice dataset,

>gset1 <- getGEO("GSE46268", GSEMatrix =TRUE)
>if (length(gset1) > 1) idx <- grep("GPL570", attr(gset1, "names")) else idx <- 1
>gset1 <- gset1[[idx]]

> str(exprs(gset1))
 num [1:54675, 1:12] 9.29 9.25 11.32 10.66 6.07 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:54675] "1007_s_at" "1053_at" "117_at" "121_at" ...
  ..$ : chr [1:12] "GSM1127890" "GSM1127891" "GSM1127892" "GSM1127893" ...

My I notice that my data has no expression values? ie the ..$ is NULL. How can I solve this?

JS Low
  • 33
  • 5
  • 1
    When asking for help, you should include a simple [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) with sample input and desired output that can be used to test and verify possible solutions. – MrFlick Aug 03 '18 at 15:36
  • Sorry about that, I edited the question to contain all the codes up till the point – JS Low Aug 03 '18 at 15:42
  • What packages are you using? `getGEO` isn't a base R function. – MrFlick Aug 03 '18 at 15:57
  • I use this one: >source("http://bioconductor.org/biocLite.R") >biocLite("GEOquery") – JS Low Aug 03 '18 at 16:51

0 Answers0