Pulling specific variables
0
0
Entering edit mode
3 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 • 200 views
ADD COMMENT
1
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)
ADD REPLY
0
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.

ADD REPLY

Login before adding your answer.

Traffic: 1400 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