I am a newbie working with R, so please excuse some potential confusion.
I have some CEL raw files and would like to generate a table with expression levels. My CEL data is based on a Clariom S Mouse CHIP.
I used the oligo package to import and read my CEL files, which gives my a Large ExpressionFeatureSet. I created a matrix using:
exp_raw <- log2(Biobase::exprs(raw_data))
For the obtained matrix I get unspecified features (just numbers starting from 1...). I would like to assign the features to the Clariom S Mouse data CHIP that was used (meaning the gene names from the CHIP). Is there an easy way to do that?
In addition to that I can do some simple quality analysis but I don’t know how I can define groups for my samples, to compare them (I have 6 samples and two different genotypes that I want to compare). Do you have a recommendation how to deal with that? Do I need to create some Array Design Format (ADF) or Sample and Data Relationship Format (SDRF)?
Thank you very much in advance! I am happy for every advice!