I´m doing my first MDA using the GEO dataset 5583 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5583)
Excuse my ignorance. What I´ve found it´s that most of the tutorials performing MDA usually use a file called targets.txt to create an AnnotatedDataFrame. This file looks something like this.
Sample Ids SampleIDs Group Apocrine.grade AR.repeat.length
However, I couldn´t find where to download this targets.txt. My questions is:
is there somewhere to download it, and how? or do I have to create it?
So in order to give a hint of where am I right now. First of all I downloaded the expressionSet using
getGEO(), but I found hard to perform the analysis with this data alone whatsoever, as some functions are not designed for expressionSet data type, like rma, etc (I suppose they´re already preprocessed anyway). Then I downloaded CEL files and I created an AffyBatch datatype and called it rawData. So I guess this rawdata is like the assay dataset from expressionSet and I´m lacking the phenotype dataset, which is essentially achieved using the targets.txt. Could I use the phenotypeDataset to create my own targets.txt; or could I use this phenotypeDataset directly?
I´ll keep trying to figure it put, but any insight would be really appreciated it. Thx!!