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Annotate text format expression data with bgx file

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.

r bgx
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updated by Kevin Blighe Kevin Blighe • written by mirzanahal • mirzanahal

1 answer

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

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written by Kevin Blighe Kevin Blighe

Thank you so much. I would follow the procedure.

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written by mirzanahal • mirzanahal

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