Gene dataset turned into NA after I tried to match probe sets to genes

Question

[ruslanovna.kim]

I am using the GitHub tutorial https://github.com/icnn/Microarray-Tutorials/wiki/Affymetrix#4-batch-correction

Every code was perfect and I got exact expected results as in the tutorial. However, on the step 8. Annotating Probes, I ran:

to_keep <- is.na(geneDat$ensembl_gene_id) == FALSE)

geneDat <- geneDat[to_keep,]

datAll <- datAll[to_keep,]

my whole data "geneDat" turned into NA https://postimg.org/image/8bm09qizr/ instead of the example provided in the tutorial of what it should be.

I don't have enough experience to know whether the tutorial missed something or something is wrong on my end. I followed every code exactly, so can't understand what's the problem.

Thanks for help!

[Jean-Karim Heriche]

Most likely it's a problem with mapping the probes to EnsEMBL genes. If all values are NA, I would suspect that you didn't have access to EnsEMBL data. Check the biomaRt user guide especially if you're behind a proxy.

[ruslanovna.kim]

Thank you, I fixed the problem. I believe that was the problem you described.