Hi!
This post is related to something I posted before christmas, but as a follow up.
This is my design tested with edgeR.
> time2.healthy <- as.numeric(status=="Control" & timepoints==2)
> time2.diabetic <- as.numeric(status=="pT2D" & timepoints==2)
> design <- model.matrix(~patients+time2.healthy+time2.diabetic)
> colnames(design)
[1] "(Intercept)" "patients2" "patients4" "patients8"
[5] "patients13" "patients17" "patients21" "patients53"
[9] "patients55" "patients61" "patients62" "patients67"
[13] "patients70" "patients71" "patients72" "patients73"
[17] "patients75" "patients76" "patients77" "patients79"
[21] "patients81" "patients82" "patients83" "patients86"
[25] "patients87" "patients88" "time2.healthy" "time2.diabetic"
lrt <- glmLRT(fit, contrast=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-1,1))
(Meaning "time2.diabetic" - "time2.healthy")
We have now measured one protein we found from this results, now I want to analyse the result "the same way".
I therefore cleared my workspace, made a matrix with the protein results and the same model.matrix I ran edgeR with. I then ran:
fit <- glm.fit(design,dataframe$myGene)
Question is where do I go from here?
This post is related to something I posted before christmas, but as a follow up.
This is my design tested with edgeR.
> time2.healthy <- as.numeric(status=="Control" & timepoints==2)
> time2.diabetic <- as.numeric(status=="pT2D" & timepoints==2)
> design <- model.matrix(~patients+time2.healthy+time2.diabetic)
> colnames(design)
[1] "(Intercept)" "patients2" "patients4" "patients8"
[5] "patients13" "patients17" "patients21" "patients53"
[9] "patients55" "patients61" "patients62" "patients67"
[13] "patients70" "patients71" "patients72" "patients73"
[17] "patients75" "patients76" "patients77" "patients79"
[21] "patients81" "patients82" "patients83" "patients86"
[25] "patients87" "patients88" "time2.healthy" "time2.diabetic"
lrt <- glmLRT(fit, contrast=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-1,1))
(Meaning "time2.diabetic" - "time2.healthy")
We have now measured one protein we found from this results, now I want to analyse the result "the same way".
I therefore cleared my workspace, made a matrix with the protein results and the same model.matrix I ran edgeR with. I then ran:
fit <- glm.fit(design,dataframe$myGene)
Question is where do I go from here?
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