I am attempting to analyse RNA-seq data using either edgeR or DESeq2 to determine differentially expressed genes. The experimental conditions are as follows:
Mice were either fed a high fat diet or a low fat diet.
Each cage had 3 mice in it, but each group has a total of 6 mice. (i.e., for the low fat diet, there are 6 mice, which have come from 2 different cages).
Therefore, I am attempting to correct for any batch effects due to the different cages the mice were raised in, this is where I am having a problem.
Essentially, I have the following: ( I have attached an image of the table too)
sample treatment cage
1 low 1
2 low 1
3 low 1
4 low 2
5 low 2
6 low 2
7 high 3
8 high 3
9 high 3
10 high 4
11 high 4
12 high 4
I have attempted to include this fact into a design matrix but I keep getting the same error of incomplete rank. I know the experimental design is not ideal, but it is what we have to work with.
If anyone has any ways of correcting for the different cages, that would be great.
Thanks for any help,
E
Mice were either fed a high fat diet or a low fat diet.
Each cage had 3 mice in it, but each group has a total of 6 mice. (i.e., for the low fat diet, there are 6 mice, which have come from 2 different cages).
Therefore, I am attempting to correct for any batch effects due to the different cages the mice were raised in, this is where I am having a problem.
Essentially, I have the following: ( I have attached an image of the table too)
sample treatment cage
1 low 1
2 low 1
3 low 1
4 low 2
5 low 2
6 low 2
7 high 3
8 high 3
9 high 3
10 high 4
11 high 4
12 high 4
I have attempted to include this fact into a design matrix but I keep getting the same error of incomplete rank. I know the experimental design is not ideal, but it is what we have to work with.
If anyone has any ways of correcting for the different cages, that would be great.
Thanks for any help,
E
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