Answers.Body: <p>There are a number of factors to consider when doing a pathway Over Representation Analysis (ORA), in particular for metabolomics. I recommend an overview such as <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8448349/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8448349/</a></p>
  <p>This covers concepts such as correcting for multiple hypotheses (as well as other considerations). You should always do this to avoid false positives (i.e don’t use the raw p values). Note that whichever correction method you use for your results, none of the pathways are significant, so the specifics are somewhat moot for these results. But even when you do have significant corrected p-values, overrepresented should be treated as hypotheses.</p>
  
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Answers.CreationDate: 2024-08-17T18:55:32.043Z
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Answers.UserDisplayName: Chris Mungall
Body: <p><a href="https://i.sstatic.net/oTGKhjpA.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/oTGKhjpA.jpg" alt="enter image description here" /></a>MetaboAnalyst pathway analysis results give a total of 4 different p-values viz, <strong>raw p-value</strong>, <strong>-log10 pvalue</strong>, <strong>Holm-Bonferroni adjusted p-value</strong> and the <strong>FDR value</strong>. And an impact score.</p>
  <p>Which value should be considered in my case (above image) to get significant pathways? And what should be the threshold cut off?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-16T09:32:31.233Z
Comments.Text: It is best recommended not to upload a picture of text as it becomes hard to read and reproduce. Instead, create a table using MarkDown (As shown here - https://meta.stackexchange.com/questions/356997/new-feature-table-support). If the image is from a journal/article, please list the article and table number so people can access it and help you better.
Comments.UserDisplayName: Karthik Nair
Tags: <pathway><mass-spectrometry><p-values><multi-omics>
Title: What parameter and threshold to choose to get significant pathways from MetaboAnlyst pathway analysis results?
ThreadText: # What parameter and threshold to choose to get significant pathways from MetaboAnlyst pathway analysis results?
  
  (Asked by: username_0 on 2024-08-16)
  
  [![enter image description here](https://i.sstatic.net/oTGKhjpA.jpg)](https://i.sstatic.net/oTGKhjpA.jpg)MetaboAnalyst pathway analysis results give a total of 4 different p-values viz, **raw p-value**, **-log10 pvalue**, **Holm-Bonferroni adjusted p-value** and the **FDR value**. And an impact score.
  
  Which value should be considered in my case (above image) to get significant pathways? And what should be the threshold cut off?
  
  **Tags:** pathway, mass-spectrometry, p-values, multi-omics
  
  > **Comments:**
  > **username_1**: It is best recommended not to upload a picture of text as it becomes hard to read and reproduce. Instead, create a table using MarkDown (As shown here - https://meta.stackexchange.com/questions/356997/new-feature-table-support). If the image is from a journal/article, please list the article and table number so people can access it and help you better.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2024-08-17. Score: 0
  
  There are a number of factors to consider when doing a pathway Over Representation Analysis (ORA), in particular for metabolomics. I recommend an overview such as <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8448349/>
  
  This covers concepts such as correcting for multiple hypotheses (as well as other considerations). You should always do this to avoid false positives (i.e don’t use the raw p values). Note that whichever correction method you use for your results, none of the pathways are significant, so the specifics are somewhat moot for these results. But even when you do have significant corrected p-values, overrepresented should be treated as hypotheses.
  
  
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