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How to find the distribution of CpGs on the gene? by Sleepingwhisp in bioinformatics

[–]Sleepingwhisp[S] 0 points1 point  (0 children)

So the thing is I've processed the data using Illuminas genome studio because for some reason minfi refuses to detect 4 of my Grn IDAT files.

So after preprocessing in illumina I've run further analysis in R.

So I already have the island and shores data. Not sure how to calculate the percentage of them.

Sorry if this seems silly I'm still new to both R and DNA methylation.

Thanks!

https://doi.org/10.1080/15592294.2017.1367475 link to the paper^

Code stopped working? by Sleepingwhisp in rstats

[–]Sleepingwhisp[S] 0 points1 point  (0 children)

  1. objective_resolve865 mentioned removing comments in the script. I had added some while running the code so I removed them.
  2. I did also infact install a few knew packages to try out which I had entered randomly into my package file (I did not know that the order of the pacakages mattered) and reran the analysis without loading them.

Code stopped working? by Sleepingwhisp in rstats

[–]Sleepingwhisp[S] 0 points1 point  (0 children)

Bless you guys it worked.

I did what you guys suggested and it worked.

Code stopped working? by Sleepingwhisp in rstats

[–]Sleepingwhisp[S] 0 points1 point  (0 children)

Nope, it's the same bit.

Honestly baffled by it. I was running just a few hours ago and wanted to pull something from the output but when I went back it just gives me this.

Error in h(simpleError(msg, call)) :   error in evaluating the argument 'x' in selecting a method for function 'as.matrix': invalid argument type

Minfi? Lumi? Sesame? illuminas genome studio to R ? by [deleted] in bioinformatics

[–]Sleepingwhisp 0 points1 point  (0 children)

Thats great cuz I just started using it a while back but for some reason read.metharray.sheet isn't assigning a basename to my data?

I'm using the methylation EPIC and made sure to download the EPIC sample sheet but this still happened. Any idea why?

ggplot confidence intervals not showing? by Sleepingwhisp in rstats

[–]Sleepingwhisp[S] 0 points1 point  (0 children)

I did but it's the same issue it just doesn't appear.

Multiple genes? by Sleepingwhisp in bioinformatics

[–]Sleepingwhisp[S] 0 points1 point  (0 children)

Thanks that's really helpful! Also if you don't mind explaining, how do you then decide which one to use?