User: Simone

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Simone170
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Posts by Simone

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Comment: C: IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kP
... Wow, Tim, thank you so much, this code works perfectly! I think I never received from anybody a code directly and completely working ... And you are definitely right, I have to learn how to use all the GRanges stuff, it seems to be really flexible. Will work through the vignette! Again, thank you f ...
written 5.8 years ago by Simone170
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Comment: C: IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kP
... Dear Tim, Thanks a lot for your comprehensive reply. The code you posted seems quite complicated, I'll have a closer look on it tomorrow. I am just writing already now to tell you that I made a mistake in my previous posting: I did not mean IlluminaHumanMethylation450kPATH2PROBE, but IlluminaHumanM ...
written 5.8 years ago by Simone170
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Answer: A: IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kP
... > Does anyone know why Jim's lines of code do not work on my R installation > (R3.0.1)? > > library(FDb.InfiniumMethylation.hg19) > x <- get450k() > Error in `seqinfo<-`(`*tmp*`, value = NULL) : > the supplied 'seqinfo' must be a Seqinfo object > In addition: Warning ...
written 5.8 years ago by Simone170
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Comment: C: IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kP
... Dear Tim, > You will need to use toggleProbes() to get all probe locations (this is an > undesirable side effect of the db0 package infrastructure, which is geared > towards expression arrays where probes that map to multiple accessions are a > "bad thing", and that is the reason I depr ...
written 5.8 years ago by Simone170
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Comment: C: IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kP
... Dear James, > You would be better off using the FDb.InfiniumMethylation.hg19 package, > which not only has all the locations for the probes, but also has them in a > more useful format. > >> library(FDb.InfiniumMethylation.hg19) >> x <- get450k() Thanks for the suggestio ...
written 5.8 years ago by Simone170
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IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?
... Hello! A little question: I've got a table with beta values obtained by Illumina's 450K BeadChip microarray and want to know for each probe where in the gene it is located (mainly promoter region or gene body). I found the IlluminaHumanMethylation450kPROBELOCATION function in the IlluminaHumanMethy ...
microarray illuminahumanv2 written 5.8 years ago by Simone170 • updated 5.8 years ago by Tim Triche4.2k
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Answer: A: DEXSeq: Problems trying to reproduce the example of the vignette
... Dear Ashu, well, the fix was what Wolfgang Huber wrote - running the code of the function contained in DEXSeq to have it in the workspace. This one works. I paste Wolfgang's reply here again: > Your problem with 'plotDispEsts' is an oversight of ours > in the last release of the DEXSeq packa ...
written 5.8 years ago by Simone170
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Comment: C: DEXSeq: Problems trying to reproduce the example of the vignette
... Dear Wolfgang, thank you very much for your reply. > plotDispEsts > as a workaround, please run the R code in the vignette from the > .R file provided with the package I missed this! Now it works fine. > I am not sure I understand your problem with 'plotMA'; what do you get from > ...
written 5.9 years ago by Simone170
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DEXSeq: Problems trying to reproduce the example of the vignette
... Hi! As the subject says, I've got some problems with DEXSeq. For the moment, I am just trying to reproduce the example of the Vignette. The first error that occurrs is when I try to plot the per-gene disperion estimates using plotDispEsts: > library("DEXSeq") > library("pasilla") > librar ...
dexseq written 5.9 years ago by Simone170 • updated 5.9 years ago by Wolfgang Huber13k
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Comment: C: Analyzing "differential variability" of methylation (and gene expression)
... > This was for charm data: > http://biostatistics.oxfordjournals.org/content/13/1/166 > but could be a starting point after adjusting for cell-types? As > implemented (http://biostat.jhsph.edu/~ajaffe/code/vmrFinder.R) , it > only allows for dichotomous covariate. Yes, I know this (v ...
written 6.0 years ago by Simone170

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Popular Question 22 months ago, created a question with more than 1,000 views. For Perform limma on a subset of genes of interest

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