User: maden.sean

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maden.sean10
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United States
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10 months, 2 weeks ago
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3 years, 8 months ago
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Posts by maden.sean

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Giemsa stain annotation/nomenclature for UCSC cytoband tracks
... That's a fair point. My question comes up because I've noticed the cytobands being used in documentation for several Bioconductor packages, and I'm interested in the Giemsa Stain cytobands specifically, not UCSC tables in general. I will direct my question to UCSC as well. Sean  ...
written 2.1 years ago by maden.sean10
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Giemsa stain annotation/nomenclature for UCSC cytoband tracks
... Hi, Background: This is a general question regarding UCSC's provided cytoband info, specifically whole-genome Giemsa Stain track information, as provided here: https://genome.ucsc.edu/cgi-bin/hgTables (assembly = hg19; group = Mapping and Sequencing; track = Chromosome Band (ideogram); type = cyto ...
ggbio gviz ucsc hg19 ucsctrack written 2.1 years ago by maden.sean10 • updated 2.1 years ago by maximilianh10
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Comment: C: Covert MethylSet to RGChannelSet object
... Kasper, Thanks for your reply. I was hoping that, despite the missing data, I would be able to fill in the limited data I have in order to perform normalizations that don't require the other kinds of probes and intensities.  Sean ...
written 2.6 years ago by maden.sean10
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Covert MethylSet to RGChannelSet object
... Hi there, I'm interested in converting a MethylSet back to an RGChannelSet object for purposes of preprocessing (I am using unprocessed data obtained from GEO), but I'm unsure of how to do this. My understanding is that preprocessRaw() uses manifest info to associate idat channels with the correct ...
minfi hm450 written 2.6 years ago by maden.sean10 • updated 2.6 years ago by Kasper Daniel Hansen6.4k
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Comment: C: Error in loading GenomicMethylSet: "no slot of name 'elementMetadata' for this o
... Thanks for the reply, Kasper. I will add this step to my workflow. cheers, Sean ...
written 3.4 years ago by maden.sean10
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Error in loading GenomicMethylSet: "no slot of name 'elementMetadata' for this object of class 'GenomicMethylSet'"?
... Hi all, This is a new error I haven't experienced in eight months working with minfi, until last week. When attempting to load a GenomicMethylSet, either as part of an environment or as an individual .rda file, I receive the following error message:  Error in nrow(x@elementMetadata) : error in ...
minfi written 3.4 years ago by maden.sean10 • updated 3.4 years ago by Kasper Daniel Hansen6.4k
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Answer: A: HM450k annotation error and warning with getAnnotation() and manual install
... False alarm folks - I made a typo in attempting the manual install. Still not sure why my libraries needed to be manually reinstalled, but at least I know the problem isn't with minfi and I can successfully run getAnnotation(). S ...
written 3.4 years ago by maden.sean10
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Comment: C: Setting seed in preprocessSWAN and random probe selection within and between arr
... This makes sense, thank you. best, Sean ...
written 3.4 years ago by maden.sean10
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Comment: C: Setting seed in preprocessSWAN and random probe selection within and between arr
... Thank you very much for your reply.  I notice an error thrown when I attempt to normalize a single array using preprocessSWAN(), which seems like it shouldn't happen if the normalization is only at the intra-array level (please see below).  Am I correct in that you are referring to the Functional ...
written 3.4 years ago by maden.sean10
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Setting seed in preprocessSWAN and random probe selection within and between arrays
... Hello all, I am interested in details about the random component in probe selection at both the intra- and inter-array levels for preprocessSWAN() in minfi.  From the original paper I don't notice any explanation of explicit inter-array normalization, just that the intra-array normalization reduce ...
minfi written 3.4 years ago by maden.sean10 • updated 3.4 years ago by James W. MacDonald49k

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