Hi!
The EdgeR manual is quite nice, but I dont quite understand what the model.matrix for EdgeR actually will test!
status <- factor(c(rep("Diabetic",22), rep("Healthy",26)), levels=c("Diabetic","Healthy"));
patients <- factor(c(04,21,53,55,61,62,67,73,76,77,79,04,21,53,55,61,62,67,73,76,77,79, 01,08,13,70,71,72,75,81,82,83,86,87,88,01,08,13,70,71,72,75,81,82,83,86,87,88));
timepoints = as.factor(c(1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2));
targets <- data.frame(Status=status, patient=patients, timepoint=timepoints)
design <- model.matrix(~patients + timepoints*status);
colnames(design)
> colnames(design)
[1] "(Intercept)" "patients4"
[3] "patients8" "patients13"
[5] "patients21" "patients53"
[7] "patients55" "patients61"
[9] "patients62" "patients67"
[11] "patients70" "patients71"
[13] "patients72" "patients73"
[15] "patients75" "patients76"
[17] "patients77" "patients79"
[19] "patients81" "patients82"
[21] "patients83" "patients86"
[23] "patients87" "patients88"
[25] "timepoints2" "statusHealthy"
[27] "timepoints2:statusHealthy"
What I want is to look if diabetics has changed genes at timepoint 2 compared to healthy (I have done this with DESeq2, just want to check if they match).
Will: [27] "timepoints2:statusHealthy" Give me what I want?
Any input?
Thanks!
The EdgeR manual is quite nice, but I dont quite understand what the model.matrix for EdgeR actually will test!
status <- factor(c(rep("Diabetic",22), rep("Healthy",26)), levels=c("Diabetic","Healthy"));
patients <- factor(c(04,21,53,55,61,62,67,73,76,77,79,04,21,53,55,61,62,67,73,76,77,79, 01,08,13,70,71,72,75,81,82,83,86,87,88,01,08,13,70,71,72,75,81,82,83,86,87,88));
timepoints = as.factor(c(1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2));
targets <- data.frame(Status=status, patient=patients, timepoint=timepoints)
design <- model.matrix(~patients + timepoints*status);
colnames(design)
> colnames(design)
[1] "(Intercept)" "patients4"
[3] "patients8" "patients13"
[5] "patients21" "patients53"
[7] "patients55" "patients61"
[9] "patients62" "patients67"
[11] "patients70" "patients71"
[13] "patients72" "patients73"
[15] "patients75" "patients76"
[17] "patients77" "patients79"
[19] "patients81" "patients82"
[21] "patients83" "patients86"
[23] "patients87" "patients88"
[25] "timepoints2" "statusHealthy"
[27] "timepoints2:statusHealthy"
What I want is to look if diabetics has changed genes at timepoint 2 compared to healthy (I have done this with DESeq2, just want to check if they match).
Will: [27] "timepoints2:statusHealthy" Give me what I want?
Any input?
Thanks!
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