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Old 08-22-2013, 11:35 PM   #1
NicoBxl
not just another member
 
Location: Belgium

Join Date: Aug 2010
Posts: 264
Default DESeq2 error : the model matrix is not full rank

Hi,

I've got an error in a DESeq2 analysis. So I've 30 samples, with a 3 factor design. So I put a Replicate column in my design . it's for technical replicate. I don't know if it's a good idea...

So when I use DESeq2 :

Code:
dds <- DESeqDataSetFromMatrix(countData=OAR.readCount,colData=design,design= ~ Stranded + Replicate + condition )
and I have an error :

invalid class “DESeqDataSet” object: the model matrix is not full rank, i.e. one or more variables in the design formula are linear combinations of the others

Anyone has an idea to solve this ?

Thanks,

N.

Code:
Sample	condition	Stranded	Replicate
A.1	Ctrl	No	A
B.1	Ctrl	No	B
C.1	Ctrl	No	C
D.1	Tum	No	D
E.1	Tum	No	E
F.1	Tum	No	F
G.1	Tum	No	G
H.1	Tum	No	H
I.1	Tum	No	I
J.1	Tum	No	J
K.1	Tum	No	K
L.1	Tum	No	L
M.1	Ctrl	Yes	M
N.1	Tum	Yes	N
O.1	Tum	Yes	O
P.1	Tum	Yes	P
E.2	Tum	Yes	E
F.2	Tum	Yes	F
I.2	Tum	Yes	I
Q.1	Tum	Yes	Q
K.2	Tum	Yes	K
R.1	Tum	Yes	R
S.1	Tum	Yes	S
T.1	Tum	Yes	T
L.2	Tum	Yes	L
O.2	Tum	Yes	O
T.2	Tum	Yes	T
I.3	Tum	Yes	I
L.3	Tum	Yes	L
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