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  • DESEQ2 design matrix help

    Hello:

    I have a complicated RNASeq experimental design and I need some help from experts.

    my aim is to compare normal vs. tumor rna-seq data.

    I have 4 different normal samples obtained from two different sites of two different animals.

    Similarly I have 9 tumor samples. 6 of them were obtained from 3 different animals (from 2 sites). 3 samples from 3 different sites of a single mouse.

    Normal
    N1 - animal 1
    N2 - Animal 1

    N3 - Animal 2
    N4 - Animal 2

    Tumor:

    T1 - Animal 1
    T2 - Animal 1

    T3 - Animal 2
    T4 - Animal 2

    T5 - Animal 3
    T6 - Animal 3

    T7 - animal 4
    T8 - animal 4
    T9 - animal 4


    Using DESeq2, how can this model be fitted for identifying differentially expressed genes between normal and tumors.

    thanks

  • #2
    Conditions = (Normal and Tumor)
    Genotype = (Animal1, Animal2, Animal3, Animal4)
    DESeq equation ~ Conditions + Genotype

    One concern/question is how do you want the comparison to be ?

    Comparison 1: Normal_Animal1 vs Tumor_Animal1
    Comparison 2: Normal_Animal2 vs Tumor_Animal2
    Comparison 3: Normal_Animal1+Normal_Animal2 vs Tumor_Animal1+Tumor_Animal2 (I am not sure if this is correct)
    Comparison 4: Normal_Animal1+Normal_Animal2 vs Tumor_Animal1+Tumor_Animal2+Tumor_Animal3+Tumor_Animal4 (I am very skeptical about this comparison because you are not comparing apples to apples..)

    Comment

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