Expression data missing in a GEO study
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Entering edit mode
6.6 years ago
William ★ 4.8k

I am downloading  GEO datasets using GEOQuery in bioconductor.

For most GEO datasets this works well.

For GEO GSE39278 however no expression data is parsed from the GEO dataset. 

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39278

The R code that I am using is below. The study is downloaded and the metadata is parsed succesfully. The expression table however only contains the sample id's and no probes or expression data.

Is there something wrong with the dataset or am I missing something in GEOquery?

library(GEOquery)
geo_id <- "GSE39278"
gseList <- getGEO(geo_id)
gse <- gseList[[1]]
pd <- pData(gse)
names(pd)
head(pd)
expressionTable =  exprs(gse)
expressionTable

 

GEOquery bioconductor GEO • 3.2k views
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1
Entering edit mode
3.8 years ago

I found this old unanswered post while troubleshooting.

I had the same problem for some other GEO data sets (GSE46691, GSE79956, GSE79957, GSE62667). The explanation, given by GEO-support, for the missing data is that the file accessed by getGEO ("series_matrix" or "soft" in the GEO record) does not contain processed data for a few records, or only contain a subset of the data (for unclear reasons). However, full processed data may be provided as supplementary files instead.

The GEO data set queried by William, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39278, does not seem to have processed data available at all (see "Processed data not provided for this record" at the bottom). However the CEL files are available.

So this is more a feature of GEO and not a bug in GEOquery.

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