Question: Differentially Expressed genes analysis
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gravatar for premraj.preeti
24 months ago by
premraj.preeti0 wrote:

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 • 688 views
ADD COMMENTlink modified 24 months ago by Kevin Blighe67k • written 24 months ago by premraj.preeti0
0
gravatar for Kevin Blighe
24 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

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

ADD COMMENTlink modified 24 months ago • written 24 months ago by Kevin Blighe67k
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