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Entering edit mode
Bine ▴ 10
@bine-23912
Last seen 7 days ago
Spain

Dear all,

I believe I have understood now how the grouping of variables work:

dds$group <- factor(paste0(dds$genotype, dds$condition)) design(dds) <- ~ group dds <- DESeq(dds) resultsNames(dds)  the condition effect for genotypeIII results(dds, contrast=c("group", "IIIB", "IIIA"))  My orginal code was: dds4 <- DESeqDataSetFromMatrix(countData = cts, colData = colData, design = ~ BATCH + AGE + SEX + CONDITION  So if I use above code will my experiment not be controlled for BATCH, AGE and SEX? Or means "design(dds) <- ~ group" that i am adding "group" to " ~ BATCH + AGE + SEX + CONDITION" ... making it " ~ BATCH + AGE + SEX + CONDITION + group"? But then "condition" would be twice kind of in my formula as "CONDITON" and as "group"?! I am confused, thank you! Bine DESeq2 • 113 views ADD COMMENT 1 Entering edit mode swbarnes2 ▴ 780 @swbarnes2-14086 Last seen 16 minutes ago San Diego So if I use above code will my experiment not be controlled for BATCH, AGE and SEX? First of all are you sure that you need to control for those? Does, say, a PCA plot show that those are strong contributors to the variation? If you group doesn't look like paste0(dds$Age, dds$Batch, dds$Sex), then no those elements won't be part of the design if the design is just dds <- ~group.

Or means "design(dds) <- ~ group" that i am adding "group" to " ~ BATCH + AGE + SEX + CONDITION"

If you type design(dds), does it have batch and age and sex in it? If it only says group, then it only has whatever group is.

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Entering edit mode

Dear swbarnes,

Thank you very much for you reply. Yes I need to control for these factors, PCA plot clearly showed that.

Yes, you are right if I do only "design(dds) <- ~ group" the command design(dds4) gives me only this: ~group.

So I have done the following: dds$group <- factor(paste0(dds$Age, dds$Batch, dds$Sex,dds$genotype, dds$condition))

It takes a very long time to run, because it must be doing all comparisons between all these variables...

But is genotype and condidtion then still the variables of interest (for my differential expression) and I am just controlling for Age, Batch and Sex then?

Maybe I should instead do the following:

dds$group <- factor(paste0(dds$genotype, dds\$condition)) design(dds) <- ~ BATCH + AGE + SEX + group ?

Thank you for any hint!

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