User: chang02_23

gravatar for chang02_23
chang02_2320
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New User
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United States
Last seen:
2 months, 3 weeks ago
Joined:
3 years, 5 months ago
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c*********@yahoo.com

Posts by chang02_23

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Using edgeR on pre-post treatment control design
... > The contrast glmLRT(fit, contrast=c(rep(0,10),-1,1)) is testing for genes that react differently between pre and post for those who got the drug versus those who didn't. if a gene has a postive logFC  from the resulting topTags output. does it mean the absolute fold change between pre and pos ...
written 3 months ago by chang02_2320
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Comment: C: Using edgeR on pre-post treatment control design
... is TreatmentDrug:Patient3 then difference between patient 3 and patient 1?  ...
written 3 months ago by chang02_2320
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Comment: C: DESeq2 combining factors in contrasts
... Is this the correct way for comparing group a and average of (group b + c) resultsNames(dds) [1] "Intercept" "conditiona" "conditionb" "conditionc" results(dds, contrast=c(0,1,-0.5,-0.5)) ...
written 9 months ago by chang02_2320
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DESeq2 combining factors in contrasts
... I have a data set comprised of 3 conditions - a, b, and c. I want to compare DEG between group a and average of (group b + c), also just DEG between group a in b. In Limma, I would construct a design matrix like the following design = cbind(a=c(1,1,1,0,0,0,0,0,0), b=c(0,0,0,1,1,1,0 ...
deseq2 written 9 months ago by chang02_2320 • updated 9 months ago by Michael Love19k
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Comment: C: rtracklayer: how to view coordinates that failed liftover?
... Aha! I unlist the result so I couldn't figure out how to map each input range. Thank you. ...
written 19 months ago by chang02_2320
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rtracklayer: how to view coordinates that failed liftover?
... I am ilfting over SNV calls from hg38 to hg19 using rtracklayer. The liftover result has less number of lines that my input. How do i figure out which SNV calls failed liftover?   ...
rtracklayer written 19 months ago by chang02_2320 • updated 19 months ago by Michael Lawrence10k
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Comment: C: Determining number of signatures in SomaticSignatures
... Correct, 20 different samples. ...
written 3.1 years ago by chang02_2320
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Determining number of signatures in SomaticSignatures
... I have a 20 samples with mutations ranging from 50 to 144 to extract signatures. I don't find an inflection point to determine rank. It seems like the more ranks I use the "better" fit. i suppose with the small number of samples i have there really can't be more than 2 or 3 signatures. Also as i loo ...
somaticsignatures written 3.1 years ago by chang02_2320 • updated 3.1 years ago by Julian Gehring1.3k
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Comment: C: SomaticSignatures: Compare my datas with validated mutational signatures
... Do you mean to compare signatures(sigs) to data(signatures21) because both will return mutation motifs (e.g. CA A.A) as rows and signatures as columns? ...
written 3.1 years ago by chang02_2320
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Comment: C: Installation of SomaticSignatures
... I also run into problem with installation. It's having trouble finding ‘latticeGrob’ in gridExtra' even though I have downloaded maverick package and installed separately.  EDIT: Turns out gridExtra v2.0.0 doesn't export latticeGrob anymore. it's only available in v.0.9.1. I rollback to gridExtra 0 ...
written 3.1 years ago by chang02_2320

Latest awards to chang02_23

Popular Question 18 months ago, created a question with more than 1,000 views. For OFFICIAL_GENE_SYMBOL not an available idType in RDAVIDWebService
Popular Question 2.5 years ago, created a question with more than 1,000 views. For biomartRt: convert mouse gene symbol return multiple human gene symbol

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