What is the right design matrix in a Microarray data analysis?
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2.2 years ago

I have Microarray data with 3 sample each in uninfected_48hrs, infected_48hrs, uninfected_60hrs and infected_60hrs.

#3 sample infected_48h; 3 sample Uninfected_48h; 3 sample infected_60h &  sample Uninfected_60h

#First design matrix looks like this:

infected_48h  infected_60h  Uninfected_48h  Uninfected_60h
Uninfected_48h.1            0            0              1              0
Uninfected_48h.2            0            0              1              0
Uninfected_48h.3            0            0              1              0
infected_48h.1              1            0              0              0
infected_48h.2              1            0              0              0
infected_48h.3              1            0              0              0
uninfected_60h.1            0            0              0              1
uninfected_60h.2            0            0              0              1
uninfected_60h.3            0            0              0              1
infected_60h.1              0            1              0              0
infected_60h.2              0            1              0              0
infected_60h.3              0            1              0              0
attr(,"assign")
[1] 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$sample.levels [1] "contr.treatment" # Second design matrix Uninfected_48h infected_48h infected_60h Uninfected_60h Uninfected_48h.1 1 0 0 0 Uninfected_48h.2 1 0 0 0 Uninfected_48h.3 1 0 0 0 infected_48h.1 1 1 0 0 infected_48h.2 1 1 0 0 infected_48h.3 1 1 0 0 uninfected_60h.1 1 0 0 1 uninfected_60h.2 1 0 0 1 uninfected_60h.3 1 0 0 1 infected_60h.1 1 0 1 0 infected_60h.2 1 0 1 0 infected_60h.3 1 0 1 0 attr(,"assign") [1] 0 1 1 1 attr(,"contrasts") attr(,"contrasts")$SKN_group_int
[1] "contr.treatment"

# Which design matrix is prefer in this  scenario first design matrix or second design matrix?


Which design matrix should I used in this case and why? I am new to this design matrix concept. Please do comment and suggest thank you.

microarry designmatrix R • 515 views
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Something is not right, here. Please show all prior code, and paste samples of your metadata, if possible. Thank you.

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I was curious on which design matrix should I used/based on if I have 12 samples (3 infected_48hr, 3 uninfected, 3 infected_60hr and 3 uninfected_60hr). So I didn't paste the prior code. I think I should used the first design matrix.

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Sure, and yes, you can now conduct individual comparisons via makeContrasts() and contrasts.fit()

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2.2 years ago
JC 13k

in your first matrix, you have all cases separated, then you can compare directly [infected vs uninfected] or [48h vs 60h], or [infected_48h vs uninfected 48h].

In the second case, you are using your uninfected_48h as a base point, so your comparisons depend on that.

So, it depends on what are you asking your data to decide the best design matrix.

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Okay I got it thanks.