User: chang02_23

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chang02_2320
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New User
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United States
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1 day, 18 hours ago
Joined:
2 years, 8 months ago
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c*********@yahoo.com

Posts by chang02_23

<prev • 14 results • page 1 of 2 • next >
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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 14 days 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 15 days ago by chang02_2320 • updated 15 days ago by Michael Love15k
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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 10 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 10 months ago by chang02_2320 • updated 10 months ago by Michael Lawrence9.8k
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Comment: C: Determining number of signatures in SomaticSignatures
... Correct, 20 different samples. ...
written 2.4 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 2.4 years ago by chang02_2320 • updated 2.4 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 2.4 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 2.4 years ago by chang02_2320
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Comment: C: SomaticSignatures: Compare my datas with validated mutational signatures
... is the comparison available in the current release 2.4.5? ...
written 2.4 years ago by chang02_2320
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Comment: C: biomartRt: convert mouse gene symbol return multiple human gene symbol
... Based on the MGI database, the listed homolog is ZNF286A. http://www.informatics.jax.org/marker/MGI:2384758 ...
written 2.4 years ago by chang02_2320

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Popular Question 21 months 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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