Double nested design in DESeq2
1
0
Entering edit mode
bioinfo • 0
@bioinfo-12782
Last seen 3 months ago
United States

Hi, I am analyzing RNA-seq data with four factors: Condition (WT and MT), CellLine (2 cell lines in each condition), Replicate (3 replicates in each cell line) and library (paired pull-down and control for a replicate): total 2*2*3*2=24 samples (Table is the below). I would like to find the difference of pull-down/control (by paired) between the two conditions: WT and MT controlling CellLines. The issue is that cell lines are nested in conditions and replicates are nested in cell lines. How can I design the formula for DESeq2? Based on the DESeq vignette, I created the variable to recode cell line with two levels called "1" and "2" as the last column in the table and tried two designs: (1) Condition + Condition:CellLineSuppressed + Condition:CellLineSuppressed:Replicate + Condition:Library (2) Condition + Condition:CellLineSuppressed + Condition:Replicate + Condition:Library. Please let me know your advise !! Also, note that I didn't include a single "library" term in the design. Is it okay?

Sample Condition CellLine Replicate Library CellLineSuppressed
Sample-1 WT Wta 1 Input 1
Sample-2 WT Wta 2 Input 1
Sample-3 WT Wta 3 Input 1
Sample-4 WT Wta 1 Pulldown 1
Sample-5 WT Wta 2 Pulldown 1
Sample-6 WT Wta 3 Pulldown 1
Sample-7 WT WTb 1 Input 2
Sample-8 WT WTb 2 Input 2
Sample-9 WT WTb 3 Input 2
Sample-10 WT WTb 1 Pulldown 2
Sample-11 WT WTb 2 Pulldown 2
Sample-12 WT WTb 3 Pulldown 2
Sample-13 MT MTc 1 Input 1
Sample-14 MT MTc 2 Input 1
Sample-15 MT MTc 3 Input 1
Sample-16 MT MTc 1 Pulldown 1
Sample-17 MT MTc 2 Pulldown 1
Sample-18 MT MTc 3 Pulldown 1
Sample-19 MT MTd 1 Input 2
Sample-20 MT MTd 2 Input 2
Sample-21 MT MTd 3 Input 2
Sample-22 MT MTd 1 Pulldown 2
Sample-23 MT MTd 2 Pulldown 2
Sample-24 MT MTd 3 Pulldown 2

 

deseq2 • 762 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 4 hours ago
United States

Do you think the effect of condition is independent of cell line? If so you can can use:

mm <- model.matrix(~cellline + cellline:replicate + condition:library, colData(dds))

You then have to remove two columns from this matrix (this has to do with the fact that cellline and condition are not the same variable, and so the R function is putting in extra interactions for library = input, but once you modify the design matrix it is fine. Just remove the interactions that have libraryInput, and that should leave you with an interaction term for the pulldown / input in WT and for the ratio in MT. You can test these in results using "name" or compare them with contrast=list(..., ...).

ADD COMMENT
0
Entering edit mode

Hi Michael, thanks for your answer. I used the following scripts but got warning or error depending on design formula at the creation of deseq object. Can you check?

Script 1 generating error

deseq2.obj <- DESeqDataSetFromMatrix(countData=fCount, colData=sampleSheet ,design= ~ Library) 

mm <- model.matrix(~Line + Line:Replicate + Condition:Library, sampleSheet)

mm <- mm[,-grep("LibraryInput",colnames(mm))]

deseq2.obj <- DESeq(deseq2.obj[apply(counts(deseq2.obj),1,min)>=3,], modelMatrixType = mm)

<Error>

Error in fitBeta(ySEXP = ySEXP, xSEXP = xSEXP, nfSEXP = nfSEXP, alpha_hatSEXP = alpha_hatSEXP,  : 
  join_cols() / join_vert(): number of columns must be the same
In addition: Warning messages:
1: In if (modelMatrixType == "expanded" & !betaPrior) { :
  the condition has length > 1 and only the first element will be used
2: In if (renameCols) { :
  the condition has length > 1 and only the first element will be used
3: In if (modelMatrixType == "expanded") { :
  the condition has length > 1 and only the first element will be used
4: In if (modelMatrixType == "expanded") { :
  the condition has length > 1 and only the first element will be used
5: In if (modelMatrixType == "standard") { :
  the condition has length > 1 and only the first element will be used

Script 2 generating warning

deseq2.obj <- DESeqDataSetFromMatrix(countData=fCount, colData=sampleSheet ,design= ~ Condition + Condition: Library) 

mm <- model.matrix(~Line + Line:Replicate + Condition:Library, sampleSheet)

mm <- mm[,-grep("LibraryInput",colnames(mm))]

deseq2.obj <- DESeq(deseq2.obj[apply(counts(deseq2.obj),1,min)>=3,], modelMatrixType = mm)

<Warning>

Warning message:
In if (modelMatrixType == "expanded" & !betaPrior) { :
  the condition has length > 1 and only the first element will be used

ADD REPLY
0
Entering edit mode

You should pass the matrix to the argument “full”. See ?DESeq

ADD REPLY
0
Entering edit mode

Thanks for your answer. By the way, what if the effect of condition is dependent on cell line? there are four cell lines total: two from condition WT and two from condition MT: basically nested sample in the condition. That was why I considered two designs in the question. Could you recommend the design? 

ADD REPLY
0
Entering edit mode

But you can’t possibly estimate it because you have different cell lines for WT and MT. You’ve labeled them A-D.

ADD REPLY
0
Entering edit mode

Thanks for follow-up !! Yes, you are correct that they are different cell lines. However, that's why I used "CellLineSuppressed" in my two designs: (1) Condition + Condition:CellLineSuppressed + Condition:CellLineSuppressed:Replicate + Condition:Library (2) Condition + Condition:CellLineSuppressed + Condition:Replicate + Condition:Library. Does either look okay?

ADD REPLY
0
Entering edit mode

I’ve explained the effects that can be estimated and the design to use, and the ones that can’t be estimated. I’d suggest for further questions on why these can’t be estimated here you could discuss with a statistician.

ADD REPLY

Login before adding your answer.

Traffic: 370 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