User: ben.run974

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ben.run9740
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Posts by ben.run974

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Comment: C: Is biomaRt down?
... Hi Mike, Thanks for your help! I did try to go on the suggested page and I got that: <MartRegistry> <MartURLLocation database="ensembl_mart_94" default="1" displayName="Ensembl Genes 94" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/m ...
written 6 months ago by ben.run9740
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Is biomaRt down?
... Hi, For the last few days I have been using biomaRt with no problem but since yesterday I keep getting error messages: > getEnsemblID <- getBM(attributes = c('mgi_id', 'ensembl_gene_id'), filters = 'mgi_id', values = getGeneAnnot[, 1], mart = useMart(biomart = 'ensembl', dataset = 'mmusculu ...
biomart written 6 months ago by ben.run9740 • updated 6 months ago by Mike Smith3.8k
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Answer: A: ComBat with multiple batches
... So according to this post https://support.bioconductor.org/p/58357/#58369 I was thinking to do a 3 steps adjustment (I added Sentrix_Position as batch effect too). Does it look right (ie. model.matrix)? #1 - correct for Sentrix_ID effect bat.1<- ComBat(dat=datMval, batch=pheno$Sentrix_ID, m ...
written 3.5 years ago by ben.run9740
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Answer: A: ComBat with multiple batches
... Hi Evan, Thanks for your feedbacks. Is your sample size large enough to allow you to combine the two variables? This would probably be best if you can do it (I see six samples above, but I'm assuming this is just a small sample of the complete dataset?) My sample size is ~1500 samples. By combini ...
written 3.5 years ago by ben.run9740
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ComBat with multiple batches
... Hi, I have some 450k data for ~1000 samples. I want to use ComBat to adjust for 2 known batches. I would like to adjust for Age_Group and Sentrix_ID (cf. example below). My variable of interest is Sample_Group. I don't really know how to proceed (run ComBat twice? which is yes accordingly to old po ...
sva combat 450k written 3.5 years ago by ben.run9740
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Answer: A: ‘IlluminaHumanMethylation450k.db’ had non-zero exit status
... Thank you!! Unfortunately I'm using another package that depends on IlluminaHumanMethylation450k.db so I have to install it :) Cheers, Ben ...
written 4.8 years ago by ben.run9740
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‘IlluminaHumanMethylation450k.db’ had non-zero exit status
... Hi, I tried to install IlluminaHumanMethylation450k.db using biocLite but keep having some error messages. I have been able to install and use it in the past but I had to reinstall R in the meantime. I have checked that all dependancies are installed (methods, AnnotationDbi, org.Hs.eg.db). > s ...
illuminahumanmethylation450k.db written 4.8 years ago by ben.run9740 • updated 3.4 years ago by katwre0

Latest awards to ben.run974

Popular Question 3.1 years ago, created a question with more than 1,000 views. For ComBat with multiple batches
Popular Question 4.6 years ago, created a question with more than 1,000 views. For ‘IlluminaHumanMethylation450k.db’ had non-zero exit status

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