Question: How to analyse the gene expression matrix which I downloaded from GEO by Galaxy?
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gravatar for fanwq907
20 months ago by
fanwq9070
fanwq9070 wrote:

I downloaded the gene expression matrix from the GEO, it is excel format. In this file, there are 5 conditions. Now I want to get some data from this gene expression matrix file. How can I do this by Galaxy? I want to find differential expression gene in certain group.

Thanks a lot.

Best, WQ

galaxy • 888 views
ADD COMMENTlink modified 20 months ago by Jennifer Hillman Jackson25k • written 20 months ago by fanwq9070
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gravatar for Jennifer Hillman Jackson
20 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Upload the data in tabular format to start with (export from Excel first, or much better - skip cycling through Excel and load the tabular data from Geo into Galaxy directly as-is). Many tools in the group Text manipulation and others (Select, Filter), graph/run statistics on numerical data, and parse tabular datasets can be used for the data reduction/summary tasks.

If you need more help, please be specific. Geo data can be exported/retrieved in various formats, including custom tabular. Share a snippet of the exact tabular data (preserve format by using the "101/010" button to set display as "code" - or use something like a Gist link) - and the community here can offer advice/details about which tool/s to use.

Help at NCBI for reference: https://www.ncbi.nlm.nih.gov/geo/info/faq.html

Best, Jen, Galaxy team

ADD COMMENTlink written 20 months ago by Jennifer Hillman Jackson25k
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