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.
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:
Please let me know if the question doesn't make sense or if there's another method that I should be using.