Compare two RNA-Seq log2fc tables
2
1
Entering edit mode
10 days ago
Harumi ▴ 20

Hi,

I would like to compare two RNA-Seq tables of log2fc and obtain new values of log2fc. Is it possible?

Situation:

Parental strain and Mutant strain can not grow directly on sugarcane bagasse, so they were cultured first on glycerol for 24 h and then transfered to sugarcane bagasse and cultured for more 24 h.

I would like to know if there are differentially expressed genes between Parental strain and Mutant strain on sugarcane bagasse, although I would like to discount the interference of glycerol in this expression.

I have log2fc and adjusted p values for these comparisons:

  1. Mutant strain after 24 h glycerol in relation to Parental strain after 24 h glycerol.

  2. Mutant strain after 24 h glycerol plus 24 h sugarcane bagasse in relation to Mutant strain after 24 h glycerol.

  3. Parental strain after 24 h glycerol plus 24 h sugarcane bagasse in relation to Parental strain after 24 h glycerol.

  4. Mutant strain after 24 h glycerol plus 24 h sugarcane bagasse in relation to Parental strain after 24 h glycerol plus 24 h sugarcane bagasse.

If the gene A log2fc value is -3 is table 1 (the gene is negatively regulated in Mutant strain in relation to the Parental strain after 24 h glycerol), and then -1 in table 4, I wonder if the effect of sugarcane bagasse growth in Mutant strain was to negatively regulate gene A, in relation to the Parental strain.

Can I obtain a log2fc value and an adjusted p value for the effect of growth in sugarcane bagasse in Mutant strain in relation to the Parental strain discounting the effect of glycerol?

I searched on the internet and found maybe I could use contrast or interaction in DESeq2, although I am not sure which one to use or how to use it in my case. Can you please help me?

Thank you very much.

Harumi

RNA-Seq DESeq2 • 476 views
ADD COMMENT
3
Entering edit mode
8 days ago

If you want to compare A/C to B/C, don't. Just compare A to B. If you want to compare A/B to C/D, do interactions. This will get you fold changes and p-values.

ADD COMMENT
2
Entering edit mode
8 days ago
joe ▴ 290

I would like to compare two RNA-Seq tables of log2fc and obtain new values of log2fc. Is it possible?

You could calculate a 'fold-change difference' but something simple like a pairwise comparison and Spearman rank correlation (which also gives p-value) should be more suitable here.

To compare single genes across conditions a z-score could work .

ADD COMMENT
0
Entering edit mode

Not OP but I have run in to this issue too. What would be the appropriate way to calculate a 'fold-change difference' on these Log2fc values? Would it be (sugarcane+glycerol - glycerol) / | glycerol | ?

ADD REPLY
0
Entering edit mode

I would take only the difference. One could separately calculate a ratio, which might be more sensitive. However unless you (or OP) have a clear objective for doing this, I'm not sure there's much to be learned vs the 'traditional' z-scaled heatmap/pairwise comparison or volcano plot.

ADD REPLY
0
Entering edit mode

If you want to compare glycerol to sugarcane + glycerol, just compare them to each other.

ADD REPLY

Login before adding your answer.

Traffic: 1733 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