Hi!
Im going to try finding differential expressed genes "correlated" with a continuous variable using DESeq2.
This is the design Im using, you can see that its only one variable and its continuous. I have 26 biological replicates.
> des <- model.matrix(~GIR)
> des
(Intercept) GIR
1 1 4.401988
2 1 4.959263
3 1 4.386282
4 1 1.530456
5 1 1.806429
6 1 4.335553
7 1 4.206755
8 1 5.913078
9 1 2.427184
10 1 4.695216
11 1 8.343508
12 1 3.179318
13 1 4.197272
14 1 6.592866
15 1 8.607653
16 1 5.313869
17 1 6.416293
18 1 6.021505
19 1 5.291005
20 1 8.586633
21 1 9.803922
22 1 8.777473
23 1 8.312925
24 1 9.480470
25 1 8.782435
26 1 6.975749
attr(,"assign")
[1] 0 1
I used the "Wald" test and here is 1 gene from the results:
dds <- DESeq(ddsFullCountTable, test = c("Wald"))
res <- results(dds)
res = res[order(res$padj, na.last = NA), ]
head(res,1)
baseMean log2FoldChange lfcSE stat pvalue
<numeric> <numeric> <numeric> <numeric> <numeric>
NINJ1 286.41601 -0.12059350 0.02202829 -5.474483 4.387909e-08
Now, have I done it correctly? What have I actually answered and how to interpret the fold change?
Thank you very much!
Im going to try finding differential expressed genes "correlated" with a continuous variable using DESeq2.
This is the design Im using, you can see that its only one variable and its continuous. I have 26 biological replicates.
> des <- model.matrix(~GIR)
> des
(Intercept) GIR
1 1 4.401988
2 1 4.959263
3 1 4.386282
4 1 1.530456
5 1 1.806429
6 1 4.335553
7 1 4.206755
8 1 5.913078
9 1 2.427184
10 1 4.695216
11 1 8.343508
12 1 3.179318
13 1 4.197272
14 1 6.592866
15 1 8.607653
16 1 5.313869
17 1 6.416293
18 1 6.021505
19 1 5.291005
20 1 8.586633
21 1 9.803922
22 1 8.777473
23 1 8.312925
24 1 9.480470
25 1 8.782435
26 1 6.975749
attr(,"assign")
[1] 0 1
I used the "Wald" test and here is 1 gene from the results:
dds <- DESeq(ddsFullCountTable, test = c("Wald"))
res <- results(dds)
res = res[order(res$padj, na.last = NA), ]
head(res,1)
baseMean log2FoldChange lfcSE stat pvalue
<numeric> <numeric> <numeric> <numeric> <numeric>
NINJ1 286.41601 -0.12059350 0.02202829 -5.474483 4.387909e-08
Now, have I done it correctly? What have I actually answered and how to interpret the fold change?
Thank you very much!
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