Expression data extraction error. Logical result as expression matrix

Question

[hkarakurt]

Hello, I downloaded GSE62772 with getGEO() function of GEOquery package. I tried to extract expression data matrix but I have logical result and an empty matrix.

My codes are:

gse62772 <- getGEO("GSE62772")

https://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62772/matrix/ OK Found 2 file(s) GSE62772-GPL11154_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62772/matrix/GSE62772-GPL11154_series_matrix.txt.gz' Content type 'application/x-gzip' length 3778 bytes downloaded 3778 bytes

File stored at: C:\Users\hamza\AppData\Local\Temp\RtmpAv8tv8/GPL11154.soft GSE62772-GPL16791_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62772/matrix/GSE62772-GPL16791_series_matrix.txt.gz' Content type 'application/x-gzip' length 4717 bytes downloaded 4717 bytes

Using locally cached version of GPL16791 found here: C:\Users\hamza\AppData\Local\Temp\RtmpAv8tv8/GPL16791.soft

gse <- gse62772$GSE62772-GPL11154_series_matrix.txt.gz

exp <- exprs(gse)

show(exp)

 GSM1694954 GSM1694955 GSM1694956 GSM1694957 GSM1694958 GSM1694959 GSM1694960
 GSM1694961 GSM1694962 GSM1694963 GSM1694964 GSM1694965 GSM1694966 GSM1694967
 GSM1694968 GSM1694969 GSM1694970 GSM1694971 GSM1694972 GSM1694973 GSM1694974
 GSM1694975 GSM1694976 GSM1694977 GSM1694978 GSM1694979 GSM1694980 GSM1694981
 GSM1694982 GSM1694983

This data is not normalized. Is that can be the problem? How can I extract non-normalized data?

Thank you.

Answer 1

[Sean Davis]

The data for this GSE are available only as "supplemental files". You can use getGEOSuppFiles() to download the files. However, you will need to determine how best to get those files into R, as they are not in any "standard" format that GEOquery can guess.