Question: how to arrange data for pathway analysis ?
gravatar for Learner
3.2 years ago by
Learner 180
Learner 180 wrote:

Hello ,

I have two tricky questions and I appreciate any useful comment

1- I have 6 samples , 3 control (two of them are biological replicate) and 3 treated (two of them are biological replicate). How should I use them for pathway analysis ? for example does it make sense to do like this ?

Average the three control (A) , average the three treated replicate (B), then B/A ==> fold change is this right?

1- which pathway analysis is giving the statistical differences for a pathway, for example with IPA , you can say is a pathway significantly expressed by a set of genes or not based on p-value and z but is there any other pathway analazor which gives such results ?


genomics pathway analysis • 969 views
ADD COMMENTlink modified 3.1 years ago by igor8.6k • written 3.2 years ago by Learner 180
gravatar for Ron
3.1 years ago by
United States
Ron970 wrote:


Yes,the fold change B/A is correct. Use log2fold change of all genes to do pathway analysis. You can use GSEA from Broad institute for this.

ADD COMMENTlink written 3.1 years ago by Ron970
gravatar for igor
3.1 years ago by
United States
igor8.6k wrote:

If you would like to try other pathway analysis tools, check these previous threads for many alternatives:

ADD COMMENTlink written 3.1 years ago by igor8.6k
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