For a study in GEO, I would like to obtain the data table header descriptions, specifically the VALUE column for all samples in the study.If you go here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99511)and then scroll down and click one of the samples: let's choose GSM2644971. Then scroll down and you should see Data table header descriptions and below that you should see VALUE Normalized (provided the normalization method) Average Beta. That information is what I want.I tried using assayData() from the Biobase package but I didn't know whether the method takes a sample, a matrix of samples, or something else as a parameter. Apparently it takes a S4 and then returns some random text but I don't know how to use that random text.EDITED:For example, if I do:library(Biobase)library(GEOquery)getgeo<-getGEO(GSE99511)assayData(getgeo$GSE99511_series_matrix.txt.gz)When I use assayData() I would want it to return Normalized (provided the normalization method) Average Beta.Instead it returns:<environment: 0x110674178>Please let me know if the question doesn't make sense or if there's another method that I should be using.
Obtaining data table headers from GEO using GEOquery
r;database;bioconductor;text
The short answer is that if you are seeing information in a GEO sample, then it is the sample that you need to download and access using the appropriate method. In this case, that method is Columns():library(GEOquery)gsm <- getGEO(GSM2644971)Columns(gsm)          Column      Description1         ID_REF                                                            2         VALUE       Normalized (provided the normalization method) Average Beta3         Detection   PvalThe longer answer: you will really benefit from sitting down with the GEOquery documentation and trying to understand the objects that it uses and their methods. It is not something you can work out by trial and error for every case-by-case basis. The tutorial is a really good starting point (you will find Columns() in there, for example).