User: Alyssa Frazee

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Alyssa Frazee110
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Location:
San Francisco, CA, USA
Website:
http://alyssafrazee.com/
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@acfrazee
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Posts by Alyssa Frazee

<prev • 26 results • page 1 of 3 • next >
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Answer: A: Handling both technical and biological replicates in Ballgown
... The "system is computationally singular" error generally means that either one of the variables (in either "covariate" or "adjustvars") has the same value for every sample, or that two variables that are multiples of each other are in that list. Hope this helps! ...
written 11 days ago by Alyssa Frazee110
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Comment: C: ballgown custom models
... sorry, I used statistical jargon! usually when discussing how to interpret linear regression coefficients, "hold a variable constant" means we're assuming we're comparing two data points with the same value of that variable. For example, the brain region coefficient "holding pair constant" means it' ...
written 11 days ago by Alyssa Frazee110
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Answer: A: Ballgown with replicates and the adjustvars option
... It seems like what you are looking to do here is determine the differential expression between "C" and "Q", adjusting for everything else. I would convert your phenodata file to something like: "ids", "hpi", "exp", "rep", "sample" "CoffeR1C24", 24, "C", 1, "CoffeR1" "CoffeR1C48", 48, "C", 2, "Coffe ...
written 11 days ago by Alyssa Frazee110
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Answer: A: Ballgown Error in file(file, "rt") : invalid 'description' argument
... Hi there, this error usually means something went wrong with trying to read in the pData argument. The error comes from read.table, not from ballgown. More detail would be helpful in debugging here: * what is "pheno_data" in your example? (is it a file path?) * what are the contents of the file in ...
written 11 weeks ago by Alyssa Frazee110
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Answer: A: limma regularization on Ballgown
... The idea behind the sentence in the paper about performing regularization for small sample sizes is basically a suggestion to use the expression data from ballgown as the inputs to limma. limma requires you to generate an expression matrix, and if you would like to use their methods, you would use b ...
written 5 months ago by Alyssa Frazee110
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Comment: C: The common error with ballgown has not been solved!
... (1) the "rep" column should probably just be the a, b, c, or d. (2) the data frame you have listed (the one with "ids," "treatment," "time," and "rep") should be how you set pData. You can assign pData with "pData(bg) = data_form" (or whatever you've called that data frame).  (3) Ah, I see the exp ...
written 9 months ago by Alyssa Frazee110
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Comment: C: The common error with ballgown has not been solved!
... Seems like the ordering issue has been solved -- great! "how to correctly label different conditions and biological replicates for statistical analysis" -- in this case, it looks to me like each sample you have now is a biological replicate (i.e., that you have 11 biological replicates). If this is ...
written 9 months ago by Alyssa Frazee110
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Comment: C: The common error with ballgown has not been solved!
... I'd recommend checking the difference between `data_form$ids` and `list.files("ballgown")` -- it's telling you they're not all equal, so you should check to see what the differences are. A guess I have is that your files in your directory are ordered alphabetically, e.g.: "sample1", "sample10", "sa ...
written 9 months ago by Alyssa Frazee110
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Comment: C: IRanges error loading rsem data into ballgown
... Another possibility: is this a prokaryotic assembly? (Ballgown doesn't work if there isn't any intronic data present, unfortunately). On Mon, Feb 13, 2017 at 12:59 PM, Jeff Leek [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > ...
written 9 months ago by Alyssa Frazee110
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Comment: C: How fold change is calculated in Ballgown?
... Correct: you can't control which is the numerator and which is the denominator. If you want KO in the numerator and WT in the denominator, you can take the reciprocal after doing stattest.  ...
written 10 months ago by Alyssa Frazee110

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Scholar 20 months ago, created an answer that has been accepted. For A: polyester: adding noise to RNASeq counts?

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