Assign experimental groups and replicates within a GSE properly
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4 weeks ago
qstefano ▴ 20

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 • 200 views
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What is your expected metadata output ?

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In this example, I expect each of the 4 samples to be labeled with the group number they belong to, so a vector [1, 2, 3, 1].

Unfortunately, there is no unique attribute in the metadata. And these strings are very variable, so an extraction from the string itself is hardly reproducible

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