R and GEO
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3.0 years ago
geyucoco • 0

I can't get expression matrix from GEO database, because it is not included in series matrix files, then what should I do? Thank you anyway!

GEO • 1.2k views
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First step is adding details. Which dataset?

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the dataset is GSE126563

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That is a microarray, you cannot load this into the IGV. IGV tracks assume some kind of count data.

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If you have windows machine, install Transcriptome Analysis Console (TAC) Software, read the manual, load the cel files and install appropriate library files. Start analysis.

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3.0 years ago

It is implied that the normalised data is available via the Excel file that is listed at the bottom of the main accession page, and that the normalisation method was RMA (standard for Affymetrix 'chips'): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126563

You can now read Excel files directly into an R environment via readxl.

If you have more confidence, you could instead retrieve the raw data CEL files and re-process those.

Kevin

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