I´m trying to analyze the data from Illumina microarray using the Giovanni Coppola guide. I've also used some examples from the lumi package (bioconductor) and always use the targets file. The problem is, when I refer to the GEO page whoch contains the data I want to analyze, I don´t find any targets file available for download. Could you please tell me if that file is always needed? Thanks in advance.
Coppola guide: https://www.semel.ucla.edu/sites/default/files/coppola-lab/CoppolaExampleCode.pdf
You surely always need the information which data is from which sample. This is what is (sometimes) stored in the "targets.txt" file. In GEO this information is contained in the series matrix file ("GSExxxxx_series_matrix.txt"). The sample-specific information is stored in the rows starting with "!Sample_".
If your pipeline is based on using a "targets.txt" file, you can read (parse) the sample information from the GEO series matrix file and save it in the format of a "tragtes.txt" file so that you can plug it into your pipeline.
Hi!
Where did you find the targets.txt file please? Or using GEO series matrix file, how do you obtain this targets.txt file please?
Thank you,
Diana
The file targets refers to the sample info or metadata of your dataset. In geo, if you work with data in soft format, usually the metadata (sample info) are contained in the first rows of the matrix. You can also define a data frame with the info directly in R.
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