Hi there,
I am working with the dataset GSE126595. The authors tell us that there is information about sample treatment in the raw datafiles, but not the GSE files. I have tried packages such as affy and oligo but I cannot seem to get hold of the pheno data that I need. I simply need the GSM accession numbers and how the samples were treated. Does anyone know how I can do this?
Thanks
Kurt :)
hi, you have pressed the button "ADD ANSWER", while you should have pressed the "ADD REPLY" button right below Jame's comment. Anyway, you already have the answer to your question right on top, written by Basti, e.g.:
GEO stores phenotype data in columns with generic names such as
characteristics_ch1.5
. This means you need to explore the data by yourself to figure out where the relevant phenotype data is stored. One way to do this is to look at the first few rows of thedata.frame
object by doing:or, if you prefer, write that
data.frame
into a CSV file using the commandwrite.csv(pdat, "phenodata.csv")
, and open it with a spreadsheet browser.Thanks Robert. I'm fine gaining access to the phenotypic data using GEO query but since the author states that "raw data files include info on CD19 selection..." I'm wanting to check the CEL files, which I as I understand, contain the raw data. I am hoping that in there, there would be an extra column with more phenotypic information, perhaps on the CD19 selection. Any insight would be valuable.
Thanks
Kurtis.
I already responded to this exact question, and told you that the CEL files won't contain anything useful. If you don't believe me, it's easy enough to check for yourself.
Thanks James. Your insight is appreciated.