Question: different results with normal fit and contrast matrix fit
gravatar for Ice P
4.7 years ago by
Ice P0
United States
Ice P0 wrote:

I have a data set with loge base expression values of 90 normal and 10 tumor sample.

mydesign<- cbind(Tumor=c(rep(1,90),rep(0,10)),Control=c(rep(0,90),rep(1,10)))

Now, I proceeded with two way:

fit <- lmFit(data, design=mydesign)
fit <- eBayes(fit)

numGenes <- nrow(data)
case1.list <- topTable(fit,number=numGenes)


cont.matrix <- makeContrasts(TumorvsControl=Tumor-Control, levels=mydesign)
fit2 <- lmFit(data, design=mydesign)
fit2 <-, cont.matrix)
fit2 <- eBayes(fit2)

case2.list <- topTable(fit2,number=numGenes)

However, when i searched for a particular gene, the results are quite contrasting. e.g.

                  Tumor  Control AveExpr        F      P.Value    adj.P.Val
ENSG1 1.53268 5.134342 1.87246 1802.497 1.115791e-83 4.074213e-83

case2.list ["ENSG1",]

                    logFC AveExpr         t      P.Value    adj.P.Val        B
ENSG1 -3.601662 1.87246 -29.42565 2.183333e-53 3.353327e-49 110.5354

Could anyone please advice that with given tumor and control estimation, how log FC were obtained?



limma R • 1.8k views
ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 4.7 years ago by Ice P0

"contrast" in limma means something similar to "What conditions I want to compare".

ADD REPLYlink modified 7 months ago by RamRS27k • written 4.7 years ago by Antonio R. Franco4.5k
gravatar for Devon Ryan
4.7 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

This ends up not being a limma question, but more of a question of what a model matrix is and how it's used.

Case 1 is asking, "Is the signal in the 'Tumour' group greater than 0?" That is unlikely to be a biologically interesting question to ask.

Case 2 is asking, "Is there a difference between 'Tumour' and 'Control'?" That is a much more biologically interesting question to ask.

I would strongly discourage you from manually making model matrices until you're more familiar with them (and even then it's rarely more convenient to do so).

ADD COMMENTlink written 4.7 years ago by Devon Ryan95k

This should be the accepted answer.

ADD REPLYlink written 2.9 years ago by russhh5.4k
gravatar for Kamil
4.7 years ago by
Kamil2.0k wrote:

Please read the documentation for limma. Start with Chapter 9 on page 40.

ADD COMMENTlink written 4.7 years ago by Kamil2.0k
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