Microarray data : filtering genes with 2 fold above the control

Question

[jaqy]

Hello all,

I have calculated the log ratio with Diff expression in Genevestigator. (treatment VS mock)

Please how can I filter only the genes that showed 2-fold or more activation by phytohormones?

Please, do you have another tools allowing users to select genes with X fold above the control?

Thank you in advance

Best regards

[oliverv]

Hi jaqy,

I don't know if you are still working on this but I thought I would just mention that you can do this in Genevestigator very easily! After you have performed the Differential expression; select a log-ratio threshold of 1.000 with the slider at the bottom (this is equivlant to 2-fold up/down regulation). If you want only up regulated genes, swith the drop down in the top-right to "UP" rather than "BOTH".

Once you have done this, you should have just the list of genes that are 2-fold up/down regulated. After that, click on the "Results" menu in the top left of Genevestigator and select "Export Data...". This will let you save the filtered list to a csv file. You can then filter this for your set of phytohormones to find which genes related to them are over/under-expressed significantly.

One good reason not to use R/bioconductor or DESeq2 is that it is quite easy to incorrectly apply the differential expression algorithms and potentially use incorrectly chosen parameters. If you are a biologist and just want safe, correctly calculated p-values for your results, keep using Genevestigator!

I hope that was helpful :)

Answer 1

[Antonio R. Franco]

You have used a non very common resource for getting the list of differentially expressed genes. I mean Genevestigator. Most people use either the Tuxedo suite or R programs such as DESeq2, etc

I suggest you to import the data into a excel file if this program has provide you with a text delimited text. Filtering into excel is pretty easy, and Google is full on tutorials about it

Answer 2

[Shamim Sarhadi]

You could try with some packages in bioconductor, visit this page: https://www.bioconductor.org/packages/3.3/bioc/html/genefilter.html, there are some functions for filtering DEGs