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Update 09-metabolomics.md
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I fixed typos
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andrespan authored Aug 22, 2024
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Expand Up @@ -373,15 +373,13 @@ After this, write your email, so you know when your network is finished. Then cl
</a>

For more information about the rest of the parameters used for molecular networking:
- (visit the GNPS documentation)[https://ccms-ucsd.github.io/GNPSDocumentation/networking/]
- Also visit (Aron, A.T., Gentry, E.C., McPhail, K.L. et al. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 15, 1954–1991 (2020))[https://doi.org/10.1038/s41596-020-0317-5]
- [visit the GNPS documentation](https://ccms-ucsd.github.io/GNPSDocumentation/networking/)
- Also visit [Aron, A.T., Gentry, E.C., McPhail, K.L. et al. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 15, 1954–1991 (2020)](https://doi.org/10.1038/s41596-020-0317-5)

## Statistics analysis using FBMN STATS guide web server

Now we want to observe how different are the metabolic profiles of our samples. For that, we are going to calculate a Principal Coordinate Analysis (PCoA)

https://fbmn-statsguide.gnps2.org/

Go into
[FBMN STATS guide](https://fbmn-statsguide.gnps2.org/)

Expand All @@ -392,32 +390,32 @@ Select "Data Preparation"
</a>

In file origin select "Quantification table and metadata files".
-In the Quantification Table section, select the MZMine output file "GM_workshop_Featurelist_complete_quant.csv" This table contains the information of the two strains and the media. We want to observe how different our samples' metabolomic profiles are, in comparison with the culture media.
- in the Meta Data Table section, include our metadata file "metadata_table.tsv"
- In the Quantification Table section, select the MZMine output file "GM_workshop_Featurelist_complete_quant.csv". This table contains the information of the two strains and the media. We want to observe how different our samples' metabolomic profiles are, in comparison with the culture media.
- in the Meta Data Table section, include our metadata file "metadata_table.tsv".

<a href="../fig/FBMN-STATS_02.jpg">
<img src="../fig/FBMN-STATS_02.jpg" alt="FBMN" width="800" />
</a>

After loading your files, click "Submit Data for Statistics!"
After loading your files, click "Submit Data for Statistics!".

<a href="../fig/FBMN-STATS_03.jpg">
<img src="../fig/FBMN-STATS_03.jpg" alt="FBMN" width="800"/>
</a>

Check that your data have been properly submitted by checking that you have the "Data preparation was successful!"
Check that your data have been properly submitted by checking that you have the "Data preparation was successful!".

<a href="../fig/FBMN-STATS_04.jpg">
<img src="../fig/FBMN-STATS_04.jpg" alt="FBMN" width="800"/>
</a>

Now we should go to the "PERMANOVA & PCoA" section
Now we should go to the "PERMANOVA & PCoA" section.

<a href="../fig/FBMN-STATS_05.jpg">
<img src="../fig/FBMN-STATS_05.jpg" alt="FBMN" width="300"/>
</a>

Select Principal Coordinate Analysis
Select Principal Coordinate Analysis.

<a href="../fig/FBMN-STATS_06.jpg">
<img src="../fig/FBMN-STATS_06.jpg" alt="FBMN" width="600" />
Expand Down Expand Up @@ -447,7 +445,7 @@ Also, it is possible to observe that *Streptomyces* sp. H-KF8 metabolomic profil
<img src="../fig/FBMN-STATS_09.jpg" alt="FBMN" width="800"/>
</a>

There are several statistics that you can do using FBMN STATS guide, you can check the preprint (here)[https://doi.org/10.26434/CHEMRXIV-2023-WWBT0].
There are several statistics that you can do using FBMN STATS guide, you can check the preprint [here](https://doi.org/10.26434/CHEMRXIV-2023-WWBT0).


## Visualize the network using Cytoscape
Expand All @@ -467,7 +465,7 @@ Afterward, click on "Direct Cytoscape Preview/Download"

If your network is not Done, then we could use a previously computed network, that holds the same data that we used in this workshop

(Cytoscape)[https://cytoscape.gnps2.org/process?task=568cc93ed2e84f20b2b94bd186b48ee8#{}]
[Cytoscape](https://cytoscape.gnps2.org/process?task=568cc93ed2e84f20b2b94bd186b48ee8#{})

Click on "Download Cytoscape File", and save it in your computer

Expand Down Expand Up @@ -514,7 +512,7 @@ Select the pie chart again in "Image/Chart", and now select ISP2 and ISP2-ASW. T
We can observe that some nodes are detected mostly in ISP2. However, several angucycline-related compounds are detected almost exclusively in ISP2-ASW

<a href="../fig/cytoscape_09.jpg">
<img src="../fig/cytoscape_09.jpg" alt="FBMN" width=800"/>
<img src="../fig/cytoscape_09.jpg" alt="FBMN" width="800"/>
</a>


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