Differentially Expressed genes analysis
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6.0 years ago

Hi

I have a differential expressed genes files with Gene ID and Log fold change values.

I want to find the top 20 expressed genes using limma but as I do not have the feature counts with me it is giving me error.

Can you please suggest which tool within galaxy I can use

rna-seq • 1.3k views
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6.0 years ago

If you just have 'Gene ID' and 'Log fold change values', then, all that you can do is sort the list to see the genes that have the highest and lowest fold changes. For example, you could take the top 10 highest and lowest fold changes.

You need to have:

  • the original normalised data
  • metadata to help you understand the data
  • p-values associated with those fold changes
  • an understanding of the comparison that was performed to produce the fold changes
  • the overall and per group/condition sample n

If you have been asked to analyse a vector of fold changes by your supervisor, then you need to tell him/her that there is very little that one can do with such data.

Kevin

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