Pulling specific variables
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Entering edit mode
13 months ago
Bine ▴ 40

Hi there,

I have the variable sample.site which has different sites e.g. heart, leg, arm...

Now for some analysis I only want to look at e.g. arm. It works perfectly with

dds0_sub <- dds0[,dds0$Sample.Site == "arm"] But now I do the same with leg and I dds0_sub <- dds0[,dds0$Sample.Site == "leg"] but I get this error:

Error in designAndArgChecker(object, betaPrior) : full model matrix is less than full rank

Do you understand what is happening?

Thank you so much, Bine

deseq2 • 357 views
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Entering edit mode

What kind of object is dds0? If it's a simple data frame your syntax should work fine.

class(dds0)

Is leg actually one of the values in the column?

table(dds0$Sample.Site) For DESeq2 s it supposed to be a factor? dds0$Sample.Site <- factor(dds0\$Sample.Site)
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Entering edit mode

Sorry I should have been more clear. Yes, it is a DESEQ2 object and actually the above error appears after I run this

dds0 <- dds0_sub dds0 <- DESeq(dds0).

It seems it doesnt like the values of dds0_sub for leg.