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what does this chunk show us about GWMe?
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@Svad98
Svad98 committed Nov 28, 2021
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Expand Up @@ -114,6 +114,7 @@ colnames(idh1_idh2) <- c("IDH")
compiled <- cbind(tet, idh1_idh2)
View(compiled) # scrolled through and identified the patient/sample number that had the mutations in both TET2 and IDH
```

Do we see genome-wide hypermethylation from TET2 mutations?

```{r, TET2_vs_IDH}
Expand Down Expand Up @@ -169,3 +170,9 @@ fit3 <- eBayes(lmFit(exprs(DNAme)[, as.integer(rownames(design3))], design3))
# 10 probes for TET2:purity
```

I'm unsure of how to interpret the code above:
- The annotation/description of the designs are unclear.
- Why would we run the code this way?
- What do the probe numbers mean?
- How can this be translated into assessing genome-wide methylation?

1 comment on commit adc7453

@ShantiniqueMiller
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I took a dive into what probe numbers meant, I could be wrong but from my understanding, a positive probe result means that there is a change in the gene, chromosome or protein of interest. So it is my assumption that the number represents the amount of mutations that they recorded for either TET2 or IDH; it seems that TET2 had less than IDH; I am assuming based on the probe readout. I am not sure of how this would look for an experimental procedure though.

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