Best way to draw heatmap using Gfold deferentially expressed no replicate data
0
0
Entering edit mode
2.4 years ago
lookamrita • 0

Hi, I have two sample (Control and Test) RNA seq data (Ref: Human) after analyzing the files using Star and GATK pipeline , I Have used Gfold to check the differential expression analysis. Now I have Gfold output file of differential expression analysis. I want to draw heatmap using it. There are 475 genes which are having more than 2 log2fc, I want that genes to use in heatmap from the Gfold output file. What is the best way to draw heatmap using it? New in RNA-seq. Need help. Thanks in advance

RNA-Seq next-gen R • 734 views
ADD COMMENT
0
Entering edit mode

Please see as a starting point:

Heatmap based with FPKM values

There are plenty of posts here on Biostars. Please use the search function.

ADD REPLY
0
Entering edit mode

Even though I have log2fc value, shall I use FPKM only. Please see the example values and columns in my file. This is how it looks like:

Gene    GFOLD(2)    E-FDR   log2fdc 1stRPKM 2ndRPKM
7SK 3.63629 1   2.7294  0.0064312   0.0753654
A2ML1   8.08695 1   7.09134 0.00184317  0.47231
AADAC   2.57739 1   2.49758 0.108541    0.610544
AATK    2.68001 1   2.63272 0.0563924   0.34059
ABCA6   4.80114 1   4.7294  0.0358213   0.941189
ADD REPLY
0
Entering edit mode

You can use whatever you think is best. I linked this one for example code that you can adapt to feed in your FCs.

ADD REPLY

Login before adding your answer.

Traffic: 1155 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6