interaction model deseq2 specific DE genes
1
0
Entering edit mode
aec ▴ 90
@aec-9409
Last seen 4.5 years ago

Dear all,

I have a design with temperature (2-levels: 21º C and 24º C) and strain (3-levels: strain1, strain2, strain3) and I would like to find differentially expressed genes specific to each strain for the 24º C vs 21º C comparison. That means:

1) finding those genes that are differentially expressed in strain1 for 24ºC vs 21ºC comparison that are NOT differentially expressed for strain2 for 24ºC vs 21ºC neither for strain3 for 24ºC vs 21ºC. 

2) finding those genes that are differentially expressed in strain2 for 24ºC vs 21ºC comparison that are NOT differentially expressed for strain1 for 24ºC vs 21ºC neither for strain3 for 24ºC vs 21ºC. 

3) finding those genes that are differentially expressed in strain3 for 24ºC vs 21ºC comparison that are NOT differentially expressed for strain1 for 24ºC vs 21ºC neither for strain2 for 24ºC vs 21ºC. 

Th model I selected is using the combination of temperature and strain as a single factor: design~temperature_strain, but then I have to perform overlappings to find specific DE genes.

Is the model with interaction: design ~strain+temperature+strain:temperature, a better model to extract the desired (specific) DE genes directly? what would be the contrasts?

thanks,

deseq2 interaction model differential expression • 1.0k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 7 days ago
United States

There is not a contrast that will give you the genes which are DE in you strain but not DE in the others. Instead, I'd suggest to build these tables manually, by compiling across individual results tables. Note that we have a test in DESeq2 for "not DE", if you can specify an LFC threshold below which you can consider it practically "not DE", see here:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#tests-of-log2-fold-change-above-or-below-a-threshold

ADD COMMENT
0
Entering edit mode

ok Michael, so none of this contrasts answer my question directly right?

res = results(dds, contrast=c("temp","temp24",temp"21"))

res = results(dds, name="strain2.temp24")

res = results(dds, name="strain3.temp24")

res = results(dds, contrast=list("strain3.temp24", "strain2.temp24"))

ADD REPLY
0
Entering edit mode

No.  

ADD REPLY

Login before adding your answer.

Traffic: 632 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