Generating Gene Expression Levels from TSV files on GEO
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gallantk5 • 0
@5a9e144a
Last seen 1 day ago
Canada

Hi BioConductor Community ,

I am trying to automate the process of generating gene expression files from TSV raw series files on GEO.

Does anyone have any tips or BioConductor libraries that can generate gene expression levels from TSV files on GEO ?

I have been filtering GEO series records with the following query ("tsv"[Supplementary Files])

Thank you ,

-K

GEOquery GEO TSV • 159 views
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I believe most of the TSV files are RNA-Seq data , I need to automate the process for all tsv files on geo. The end product of what I need is what is shown in the table in the attached image. enter image description here

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@sean-davis-490
Last seen 2 days ago
United States

NCBI GEO has no standard format or file naming convention for supplementary files, at least that I know of. If you can limit yourself to human and mouse only, you may be interested in the RNA-seq Beta program described here:

In short, NCBI processes human and mouse RNA-seq data to produce downloadable count tables.

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Do you happen to know how the profile graph is generated on RNA-Seq records ? I tried to use the R code that is provided in the next tab and it is not producing the same results as the profile graph.

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I'm not sure what "profile graph" you are referring to. That said, the RNA-seq data that I linked to in this answer are not used by GEO for any of their pre-calculated graphs or for GEO2R as far as I know. If you want more information on how GEO produces the profile graphs, you can review that on their website:

Note that the GEO Profiles are based on GEO DataSets (https://www.ncbi.nlm.nih.gov/geo/info/datasets.html) which are no longer being created by GEO (since about 2016 or so).

In short, GEO profiles are for a limited subset of GEO and are no longer being produced for GEO data. The RNA-seq data linked to in my answer are not used internally by GEO for GEO datasets or profiles.

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