User: Ellen O

gravatar for Ellen O
Ellen O10
Reputation:
10
Status:
New User
Location:
Stellenbosch University
Last seen:
9 months, 1 week ago
Joined:
1 year, 12 months ago
Email:
e*****@sun.ac.za

Posts by Ellen O

<prev • 9 results • page 1 of 1 • next >
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Base caller software recommendations?
... I will be performing direct sequencing of bisulfite PCR products (dye-terminator sequencing on the ABI 3730xl). I have come across many options for software in terms of base calling, quality control and normalisation of the sequencing traces. I know that ABI recommends KB Basecaller because it accou ...
methylation sequencing written 9 months ago by Ellen O10
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Tools for quantitative comparison of differential tissue gene expression?
... I am attempting to assess the expression of a gene list in blood vs brain tissue (since we use blood as a proxy). I am struggling to find a tool/ database that has quantitative data (correlation, r^2 results) that's easily comparable between tissues. Does anyone know of something like this? I am try ...
gene expression tissue-specific written 16 months ago by Ellen O10 • updated 15 months ago by Biostar ♦♦ 20
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Determine "global" methylation from Illumina EPIC data?
... I have Illumina MethylationEPIC data for a group of samples. From looking at M- and B- value distributions, It seems a few of the samples display consistently different methylation levels across the genome (in other words it's not probe-specific). Is it possible to determine "global"/ total methyl ...
epic infinium methylation written 17 months ago by Ellen O10 • updated 17 months ago by andrew.j.skelton735.5k
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Gene sets associated with neurological functioning?
... I am looking for gene sets that are associated with schizophrenia specifically, but also related neurological functioning. What is the best way to do this apart from delving into the literature? As far as I can tell, going through GSEA's mSigDB is one way. Any other recommendations? Thanks in advanc ...
msigdb gene sets psychiatric genetics gsea written 17 months ago by Ellen O10 • updated 17 months ago by Alex Reynolds27k
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Error when changing the database for minfi dropLociWithSnps
... I am currently filtering Illumina MethylationEPIC data with minfi, which has run smoothly so far. To remove polymorphic CpGs and SBEs I use the following code: NormFlt <- dropLociWithSnps(NormFlt, snps=c("SBE","CpG"), snpAnno="SNPs.147CommonSingle") And get the following error: `Error ...
methylationepic minfi illumina snp methylation written 20 months ago by Ellen O10
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Comment: C: Illumina methylationEPIC demo data in IDAT format?
... Thanks so much Santosh, I wasn't aware there was EPIC data on GEO! ...
written 22 months ago by Ellen O10
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Illumina methylationEPIC demo data in IDAT format?
... Does anyone know of an available data set for the Illumina EPIC/ 850k array that has files in IDAT format that one can download? I am testing a pipeline before I get my own data back and would like to start with the raw files. Illumina's demo data only has three samples and I would like to test out ...
epic illumina methylation idat methylationepic written 22 months ago by Ellen O10 • updated 22 months ago by Santosh Anand4.6k
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Comment: C: Assessing DMRs between treatment groups: subtracting control group DMRs to accou
... Thanks Andrew, I will try it out! ...
written 24 months ago by Ellen O10
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Assessing DMRs between treatment groups: subtracting control group DMRs to account for "baseline" methylation
... I am currently awaiting Illumina methylationEPIC (850k) data and in the mean time figuring out how to assess DMRs with demo data. I am new to these analyses but I am making use of the Maksimovic *et al.* cross-package workflow (https://f1000research.com/articles/5-1281/v2), which I have found very u ...
illumina 850k dmr methylationepic written 24 months ago by Ellen O10 • updated 20 months ago by hongbo91920

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