R and GEO
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!
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geyucoco •
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geyucoco •
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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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First step is adding details. Which dataset?
the dataset is GSE126563
That is a microarray, you cannot load this into the IGV. IGV tracks assume some kind of count data.
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.