User: Jason Chen

gravatar for Jason Chen
Jason Chen10
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10
Status:
New User
Location:
United States
Last seen:
3 years, 9 months ago
Joined:
4 years, 2 months ago
Email:
j****@vergegenomics.com

Posts by Jason Chen

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Rare variant association analysis for exome study without controls
... It would not be ideal but if you cannot get any other exome chip data then this might be okay. Does the chip you are using include ancestry informative SNPs? I would first extract the 1000 genomes samples that match your study population. Then merge them, test for population structure (MDS plot, QQ ...
written 3.9 years ago by Jason Chen10
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Answer: A: GWAS for rare diseases?
... There are definitely a lot of rare diseases with interesting GWAS, for example just among neurodegenerative diseases, PSP, ALS, FTD, CBD all have GWAS now and are at about 10 in 100,000 population prevalence. ...
written 4.1 years ago by Jason Chen10 • updated 5 weeks ago by RamRS25k
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Answer: A: SNP not found on any SNP arrays
... What SNP is it? If it is very rare and non exonic it will probably not be found on any of the arrays. If it's relatively common then you could try imputation (see for example [BEAGLE](https://faculty.washington.edu/browning/beagle/beagle.html) or [IMPUTE2](https://mathgen.stats.ox.ac.uk/impute/imput ...
written 4.1 years ago by Jason Chen10 • updated 5 weeks ago by RamRS25k
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Answer: A: Microarray and RNA-seq different result
... I don't think you are using a cutoff for significance so it makes sense that roughly half are different. Most of your "DEG" signal is probably noise (probably, most genes will not be differentially expressed) so there is an equal chance that it will be "up" or "down" in the other datasets. I think y ...
written 4.2 years ago by Jason Chen10
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Comment: A: RMA background correction normalization only
... Are you using the expresso function in the "affy" Bioconductor package? I believe in that one, the log2 transformation is done as part of the RMA summarization step (also in medianpolish), and not in the previous steps. But, you could always check what the output looks like to make sure. ...
written 4.2 years ago by Jason Chen10 • updated 7 weeks ago by RamRS25k
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Answer: A: Combining Microarray and RNAseq data
... I would not try to normalize them together or make them comparable, they never will be. Instead maybe a non-negative matrix factorization approach or some similar algorithm could be helpful? ...
written 4.2 years ago by Jason Chen10
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Answer: A: Request for BEAGLE tutorial
... BEAGLE is quite straightforward and usually just the one line, so the documentation should suffice. I think that the real question you have is how to convert from PLINK format to VCF format (which is the only thing the newest BEAGLE can accept). For that, you could write your own script, or convert ...
written 4.2 years ago by Jason Chen10 • updated 7 weeks ago by RamRS25k
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Job: Bioinformatician at Verge Genomics (drug discovery startup), San Francisco, CA
... Who We Are: At Verge Genomics, we find cures for neurodegenerative diseases 1000x faster by applying network algorithms to genomic datasets. Founded by MD/PhDs from the world’s leading neurogenomics lab, we are building the next-generation pharmaceutical company using a data-driven, capital-efficie ...
R jobs rna-seq snp written 4.2 years ago by Jason Chen10

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