Annotate text format expression data with bgx file

Question

[mirzanahal]

Hi. I want to reanalysis GSE85934 dataset in R. The author provided two files GSE85934_non-normalized.txt and GPL6885_MouseRef-8_V2_0_R0_11278551_A.bgx.gz. I'm following the procedure here to achieve annotated gene expression. However, I don't have idat-files and I don't know how to retrieve them from .txt format. Also, I don't want to get data from *GEOquery, since I want the raw data to normalize it myself.

Thank you.

Answer 1

[Kevin Blighe]

Working with the BeadArrays that are in the public records can be difficult. The 'non-normalized' data probably looks like this data, here: A: illumina Arrays Illumina HumanHT-12 V3.0 expression beadchip reading data

So, in that case, you could follow the guidance that I give in that other thread.

Kevin

[mirzanahal]

Thank you so much. I would follow the procedure.