Annotating Illumina Microarray Datasets in R

Question

[ab123]

Hello there, I've been trying to solve this all day long, but cannot seem to find an answer.

I'm trying to add Gene annotations to Illumina microarray data sets.

Basically, these data sets come as txt files and have been loaded as read.delim into R, where they've been pre-processed and normalized. I'd now like to add annotation from either the illuminaHumanv4.db or the HumanHT-12_V4_0_R2_15002873_B.txt which was added to the original data by the researchers.

I'm not sure what to do here. Firstly, I followed the limma user guide p.90 for "Annotation". That failed because the guide ends abruptly and I'm not sure where to continue.

Lumi also doesn't help. I've tried to use LumiR to reupload the data with the annotation intact. Lumi does allow for that, but won't read txt files. I've had this issue across multiple files with Lumi.

And lastly I've attempted to add the columns of the uploaded HumanHT-12_V4_0_R2_15002873_B.txt annotation file to the normalized data.frame. But it's not working either.

Does anyone know of a good guide for this or have a few lines of code they can share to add annotation to data.frames or matrixes in R please?

Much obliged. Thank you!

Answer 1

[BioinfGuru]

I just completed annotation of files using chipPeakAnno. It is designed for chip seq data but the input is simply a bed file formatted txt file (which you already know how to import with read.delim) with gene IDs and positions...Take a look at it here: http://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

The output file contains the original file with extra columns depending on what you do e.g. nearest gene, MGI ID, GO term etc.

[ab123]

Hi Kenneth, thanks for the tip. Will try it out tomorrow and update how it went.