User: Pablo marin-garcia

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80
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United Kingdom
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1 year, 9 months ago
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4 years, 4 months ago
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Posts by Pablo marin-garcia

<prev • 9 results • page 1 of 1 • next >
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two 450K methylation array manifests. where is the difference?
... What is the difference between this two annotation files for illumina 450 methylation array? IlluminaHumanMethylation450kmanifest: annotation files for the 450k array. IlluminaHumanMethylation450kanno.ilmn12.hg19: annotation files for the 450k array.   Seems that in minfi both are used. qcRepor ...
methylation 450k written 21 months ago by Pablo marin-garcia80
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Is it possible to plot a track for each read group in a bam file with gviz without splitting the bam file into saparate bams?
... I have a Bam file with several individuals (read groups) and I would like to plot each of them in a different track with gviz. If I split the bam file and load all individual bam files I can do the task. But I wonder if is there any option to say to gviz to split the tracks by readgroup. If I plot ...
gviz bam written 3.1 years ago by Pablo marin-garcia80 • updated 3.1 years ago by Martin Morgan ♦♦ 20k
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Comment: C: how to use biomaRt with ensembl build 37
... Thanks Thomas, by the way I am a bit confuse with the circularity of BiomaRt. useMart needs a biomart datbase, If you don't know a biomart database you can list them with listMarts that needs the biomaRt object created with useMart that needs a biomart database....Doh?!.  From where can I have a lis ...
written 3.1 years ago by Pablo marin-garcia80
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Comment: C: how to use biomaRt with ensembl build 37
... Thanks Thomas, Now it connects but throws an error: > ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl", host="grch37.ensembl.org", path="/biomart/martservice") Error in useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "grch37.ensembl.org", : Incorrect BioMart nam ...
written 3.1 years ago by Pablo marin-garcia80
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how to use biomaRt with ensembl build 37
... Hello, I usually use biomart with my own perl scripts using the RESTful service and I point to "http://grch37.ensembl.org/biomart/martservice" But now I have been playing with BiomaRt during this week and  seems that biomart has changed their martservice from GRCh37 to GRCh38. I read the docs f ...
biomart ensembl grch37 written 3.1 years ago by Pablo marin-garcia80 • updated 3.1 years ago by Thomas Maurel700
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Comment: C: about GenomicRanges keepseqlevel deprecation and ggbio
... Thanks Tengfei, That would be fantastic. In the past I have been writing genome browsers with bioperl and ensembl code so gviz was more natural to me, but as a convinced ggplot user I want to add ggbio also to my toolkit, it seems a very nice package, and do many of the things that I have impleme ...
written 4.4 years ago by Pablo marin-garcia80
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Comment: C: about GenomicRanges keepseqlevel deprecation and ggbio
... Thanks Micheal, Someone know if ggbio would be fixed in devel shortly?. ggbio is not part of my toolkit yet (I wanted to add it to complement gviz, but as I need to use the 2.13 bioc, seems I will wait a bit longer ;-). I would skip genomic plotting from the packages I use or run gviz instead wh ...
written 4.4 years ago by Pablo marin-garcia80
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about GenomicRanges keepseqlevel deprecation and ggbio
... Hello, I am using R3.0 bioconductor 2.13, ggbio 1.9.2 and GenomicRanges 1.13..26 and when loading ggbio I have the following warning/error: || Loading required package: ggbio || No methods found in "GenomicRanges" for requests: keepSeqlevels, renameSeqlevels || Need speci ...
genomicranges ggbio written 4.4 years ago by Pablo marin-garcia80 • updated 4.4 years ago by Michael Lawrence9.8k
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how to do a paired analysis with minfi?
... I have been using minfi for doing differential methylation analysis, and now I have some studies with paired samples. Do minfi have a way of defining a paired analysis both in the categorical and continuous dmpFinder analysis? Under the hood minfi uses limma, so one possibility is to use the code ...
limma minfi written 4.4 years ago by Pablo marin-garcia80 • updated 2.2 years ago by James W. MacDonald45k

Latest awards to Pablo marin-garcia

Great Question 21 months ago, created a question with more than 5,000 views. For how to use biomaRt with ensembl build 37
Student 2.5 years ago, asked a question with at least 3 up-votes. For how to use biomaRt with ensembl build 37
Popular Question 3.1 years ago, created a question with more than 1,000 views. For how to use biomaRt with ensembl build 37

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