Can you make volcano plots using Ingenuity Pathway Analysis from microarray data? You can do it using RNA-seq datasets, but is there maybe somewhere a (hidden) plugin for microarray data as well?
Thanks.
Hi Joost,
it depends on the technology you're using (Affymetrix or Agilent) but in Genespring from Agilent you have the possibility to volcano plot your data, before going to IPA and see the biological implication of the results. if you want a free trial for volcano plotting, try Geneious.
fred
Thank you Frederic Lepretre ,
Does Genespring/Geneious takes into account that multiple probesets exist for single genes? It is a problem with Transcriptomics Analysis Console (TAC) from Applied Biosystems, where you also can generate volcano plots, yet based on the differentially expressed probesets instead of differentially expressed genes. (I use Affymetrix)
Thank you in advance,
Joost
Hi Joost,
genespring can analyse lot of designs (of course agilent, but also affymetrix) but analyzing multi probesets as a whole could generate lot of bias due to little to large differences in their designs and ways to produce them. I know we can do, but is it reliable, not really sure without taking it in account.
all the best
fred
You can make any Volcano plot as long as you have P-values and Fold Changes.
Hi Joost-
You can also try a tool like QIAGEN's OmicSoft Array Studio, that allows you to easily make volcano plots after running the appropriate statistical tests (usually a one-way or two-way ANOVA). You can fill out a form for a trial from here: https://www.qiagenbioinformatics.com/array-suite/
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