Assign experimental groups and replicates within a GSE properly

Assign experimental groups and replicates within a GSE properly

0

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.


R


RNASeq


GEO


Datasets


NCBI

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