User: christophersugai

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Posts by christophersugai

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M Value from Non-Normalized Methylated and Unmethylated Signal 450k
... Hi all, I'm interested in getting an M value for each cpg from an Illumina 450k array, but the data was deposited in unmethylated and methylated signal in this GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53840), is there a simple method to create the M values from this matrix, or wo ...
450k R methylation written 11 months ago by christophersugai0 • updated 11 days ago by rmf560
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Answer: A: genomics overlap python error
... I'm not sure, but this basically sounds like a Granges findoverlaps or subsetbyoverlaps job. If I had to guess, I would say it's something with that enumerate(). I would create csvs that are compatible with Granges via dplyr and just subsetbyoverlaps https://kasperdanielhansen.github.io/genbioconduc ...
written 22 months ago by christophersugai0
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Answer: A: Visualizing Expression Data in Heatmap.3
... Never used nanostring, can you even plot your fold changes (not log changes) with a heatmap? When I've tried on datasets, it either comes out that the data causes the heatmap to be all one color, or you have to have weird cutoffs and still may get a weird looking heatmap. Reason being that you'll ha ...
written 22 months ago by christophersugai0
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Answer: A: What does this heatmap represent?
... This is generally correct, although I would state it as prevalence rather than mutation rate. Mutation rate seems, to me at least, a different context than the paper. ...
written 22 months ago by christophersugai0
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Why Different naming for this 450k CpG in IlluminaHumanMethylation450kanno.ilmn12.hg19
... Hello all, I have a question regarding the annotation of cpgs in the lluminaHumanMethylation450kanno.ilmn12.hg19 library. During my analysis, a cpg with the 'Name' ch.1.xxxxxxxF (where x's are numbers) rather than the normal cgxxxxxxxx. I also happen to get another probe ch.21.xxxxxxR. What do these ...
450k illumina array methylation annotation written 2.0 years ago by christophersugai0 • updated 2.0 years ago by Charles Warden6.5k
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Comment: C: Limma matrix for multiple cell types from single individuals in disease and cont
... Thanks for the great answer and time you put into this response! I have one question, can I still use this if patients have a systemic disease, so 4 cell types and all disease vs 4 cell types and all control? Again, thanks for all the effort it helped me a ton! ...
written 2.1 years ago by christophersugai0
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Limma matrix for multiple cell types from single individuals in disease and control states
... Hello Biostars, I am analyzing 450k data in limma and I cannot figure out how to set up my matrix to get the most out of it. I am interested in a control versus disease state, which is simple enough. I also have multiple cell types from a single person, which is also simple. My question is how to se ...
450k R illumina written 2.1 years ago by christophersugai0 • updated 2.1 years ago by russhh4.2k

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