Comparing log2 fold values with in a file using a r studio program?

Question

[oqp5041]

Hi everyone!

I organized some genes with their log2 fold change values from smallest to biggest. However, our project deals with genes changing under different conditions of DMN over time. Is there a r studio or any other program that allows me to compare the specific genes that changed over time. For example, one file is control april v DMN april, and the other file is control april v DMN february. From these two files i am looking for on what genes changed over a specific time based on their log values A positive log value shows an increase in the upstream (expressed), and a negative log value shows down stream (not expressed). Is there an r studio program that allows to compare the genes that changed over time? I have posted pictures on how the files look like.

The above image is control april v dmn april

Bottom one is Control april dmn february

PLEASE provide an r package that can sort out over 39,000 genes.

Answer 1

[andrew.j.skelton73]

Why not just save the files as tab delimited text, read them into R, merge the two data frames by gene_id, then compare the fold changes? This is a quick way to do things, but I feel I should point out the importance in checking your statistics, if you're testing a hypothesis, then you should be using cuffdiff, DESeq2, Limma, etc to do the tests, there's a reason these programs exist to carry out large numbers or statistical tests.

[oqp5041]

Thank you for your answer. However, the files were ran through cuffdiff on usegalaxy by using an bias correction. I will try the packages that you recommended. I hope the packages will organize the genes on which specific genes changed over time by their log2 fold change values.