Unit of gene expression in GEO2R

Question

[sina.majidian]

Hi

As you know, in Value Distribution tab of GEO2R, you can see the distribution of expression of all genes for each sample. what is the unit of this value?

My another question is this, can I compare the value of expression of specific gene for different samples from different datasets?

Answer 1

[Kevin Blighe]

According to the GEO2R Documentation:

Value distribution

This feature allows you to calculate and view the distribution of the values for the Samples you have selected. Values are the original submitter-supplied data upon which GEO2R calculations are performed. Viewing the distribution is important for determining if your selected Samples are suitable for comparison; see Limitations and caveats for more information. Generally, median-centered values are indicative that the data are normalized and cross-comparable.

Value distributions may be viewed graphically as a box plot. The graphic can be saved by right-clicking on the image. Alternatively, the distribution can be exported as a tab-delimited number summary table.

This implies that the value distribution tab will show whatever data was uploaded by the authors of the study in which you are interested. That will most likely be normalised expression values on the log base 2 scale.

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If you want to compare across datasets, better that the same microarray was used, and, in such a situation, it would be better to obtain the raw data CEL files and process everything together. If you just want to compare 2 genes across datasets that are already normalised, then that is not good practice and you would be criticised for doing that.

Kevin

[sina.majidian]

Thank you for your response.

[Kevin Blighe]

Note that there is usually sample code provided on the GEO, i.e., code that you can use to immediately download normalised data (if it exists).

For example, if you go Here, you will see a tab for R script at the bottom. Running that code downloads an already-normalised data (log2 expression values) that can immediately be used for analysis.