DESeq2 (Different results when using interactive term equation)
1
0
Entering edit mode
LR0306 ▴ 10
@lr0306-13464
Last seen 6.6 years ago

 

Hello all,

I am trying to use DESeq2 to determine the number of main effect DEGs and interaction DEGs in a two-factor experiment, where each factor has 2 levels.

###################################################

Basically, for my coldata object below, 

> coldata

     disease vitamin treatment

NC.1     N    C        NC

NC.2     N    C        NC

NC.3     N    C        NC

NR.1     N    R        NR

NR.2     N    R        NR

NR.3     N    R        NR

VC.1     V    C        VC

VC.2     V    C        VC

VC.3     V    C        VC

VR.1     V    R        VR

VR.2     V    R        VR

VR.3     V    R        VR

I get the same results no matter which of the below three codes I use below:

dds = DESeqDataSetFromMatrix(countData = data, colData = coldata, design = ~ disease*vitamin)

dds = DESeqDataSetFromMatrix(countData = data, colData = coldata, design = ~ disease + vitamin + disease*vitamin)

dds = DESeqDataSetFromMatrix(countData = data, colData = coldata, design = ~ disease + vitamin + disease:vitamin)

disease_V_vs_N has 0 DEGs

vitamin_R_vs_C has 941 DEGs

diseaseV.vitaminR has 0 DEGs

###################################################

However, for that same coldata object, if I do the following code:

dds = DESeqDataSetFromMatrix(countData = data, colData = coldata, design = ~ disease + vitamin)

I get different values for the effects (and I get no interactive effects due to the model used):

disease_V_vs_N has 34 DEGs

vitamin_R_vs_C has 1919 DEGs

###################################################

Finally, if I rename the rows of the coldata object as follows:

> coldata

     disease vitamin treatment

N.1      N              N

N.2      N              N

N.3      N              N

N.4      N              N

N.5      N              N

N.6      N              N

V.1      V              V

V.2      V              V

V.3      V              V

V.4      V              V

V.5      V              V

V.6      V              V

And run the following code:

dds = DESeqDataSetFromMatrix(countData = data, colData = coldata, design = ~ treatment)

I know get the following:

disease_V_vs_N has 43 DEGs

###################################################

I am hoping to obtain some DEGs to look at for the disease_V_vs_N comparison, so I like the last method. However, I also need to obtain the other main effect an interactive term, which I can only do with the first method. 

My questions are:

1) Is the inconsistency across the methods surprising? For example: disease_V_vs_N comparison has 0 DEGs, 34 DEGs, and 43 DEGs across the methods. Similarly, vitamin_R_vs_C has 941 DEGs and 1919 DEGs across the methods.  

2) Is there another method to test for interaction that might reveal a different number of DEGs than the count of 0 I obtain in this case?

3) How (in)appropriate would it be for me to use the last method for my disease_V_vs_N comparison (mostly because I am hoping to have at least a handful of DEGs) and do the same procedure for the vitamin_R_vs_C comparison, but use the first method for my interactive term?

Thank you for sharing your thoughts on this matter.

DESeq2 • 506 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 1 day ago
United States

Q1: these are totally different designs with different interpretations. Take a look at the section of the vignette on interactions and otherwise I strongly recommend you meet with a statistician to discuss the proper design for your experiment if you don’t follow the difference between these after reading the material in our vignette.

Q2: No

Q3: You should pick a design based on what you want to test — so on the proper meaning of the coefficients and controlling for the right variables — and definitely not based on looking at how many genes are rejecting the null.

ADD COMMENT

Login before adding your answer.

Traffic: 905 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