Hello, I am a undergrad student at UC Davis, with no experience using the API, or SDK of the Allen Brain Institute. I am trying to create a python module, that will match patient microarray expression data to their disease, and anatomical structure. So using my module, and downloaded microarray dat…

Hi Jeremy, I read the document and the help files, but it only tells me the following. "The file Expression.csv contains expression values, calculated using zscore normalization. Each row begins with the ID of a probe. The file Columns.csv contains metadata for each column in Expression.csv, arra…

Hi @GerrikLabra . When you download expression data using a “Download this data button” you should have a zip file with four files: “Contents.txt”, “Expression.csv”, “Columns.csv”, and “Probes.csv”. Contents.txt will provide more details, but Probes.csv tells you about the probes/genes and Columns.…

Correct! Columns B,C,D,… of expression.csv correspond to rows 2,3,4,… in Columns.csv. Rows 1,2,3,… in expression.csv correspond to rows 2,3,4,… in Probes.csv and can also be matched from the id’s in column A.

What do these value even mean? Does -0.5 mean that this gene is very little expressed?

So in Brainspan. This fold change what dies this mean?

In all the atlases (including Brainspan) the fold change is the ratio of expression in the target vs. contrast structures: [image]

[image] I get this mess. But why?

You need to import them into Excel rather than directly opening, or use a text editor or a programming language. This can be resolved using a Google search.

Microarray Expression File

Technical

jeremyinseattle August 12, 2022, 7:18pm 6

These are most likely Z scores. See this post and the related post it references for more detail.

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Microarray Expression File

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