Assign experimental groups and replicates within a GSE properly
Hello everyone!
Is there a way to assign experimental groups and replicates within a GSE properly?
Metadata does not follow a standard, so it is not possible to automatically distinguish groups and replicates with the information contained (no luck in my case).
Example
GSE87071 contains 4 samples, of which one with 2 replicates. I can see that by parsing metadata:
[1] "time post release: E. coli cells immediately following release from Stationary phase t=0"
[2] "biological replicate: t=0 Replicate 1"
[1] "time post release: E. coli cells 1 hour following release from Stationary phase (t=1)"
[2] "biological replicate: Replicate 1"
[1] "time post release: E. coli cells 2 hour2 following release from Stationary phase (t=2)"
[2] "biological replicate: Replicate 1"
[1] "time post release: E. coli cells immediately following release from Stationary phase t=0"
[2] "biological replicate: t=0 replicate 2"
Do you know of an alternative way or package that can do this? Also via inference.
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