User: Alyssa Frazee

gravatar for Alyssa Frazee
Alyssa Frazee150
Reputation:
150
Status:
Trusted
Location:
San Francisco, CA, USA
Website:
http://alyssafrazee.com/
Twitter:
@acfrazee
Last seen:
3 weeks, 3 days ago
Joined:
3 years, 6 months ago
Email:
a************@gmail.com

Posts by Alyssa Frazee

<prev • 33 results • page 1 of 4 • next >
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Answer: A: error reading ballgown object
... How was the ballgown input data created? (do you have .ctab files? did you use cufflinks, stringtie, or something else)?  This looks like an issue with the formatting of one of the .ctab files used as ballgown input -- it's expecting TSV, but finding something with characters it can't parse (possib ...
written 24 days ago by Alyssa Frazee150
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Comment: C: Error in stattest function
... Please see https://github.com/alyssafrazee/ballgown#accessing-assembly-data for information on how to access the fold change information for each transcript (or gene or exon) for each sample. You will then need to write your own R code to calculate the expression fold change between the two samples ...
written 26 days ago by Alyssa Frazee150
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Answer: A: Error in stattest function
... The error message is there because it is not possible to use ballgown's stattest function when you only have one sample per condition. You cannot perform statistical inference without replicates. However, all is not lost! If you want, you can rank the genes/transcripts by fold change, for example, b ...
written 26 days ago by Alyssa Frazee150
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Answer: A: Multiple pairwise comparisons in ballgown
... Hi Rachael, ballgown doesn't do pairwise comparisons by default, but there are a few ways to force it to do it for you. The strategy you mention (running the pipeline on them pair by pair) is one option (you can use the "subset" function to make 6 ballgown objects, one with each genotype x pair trea ...
written 5 weeks ago by Alyssa Frazee150
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Answer: A: Error in reading ballgown object
... Hi there -- the error message means that the first column of pData (pheno_data, as you've called it) needs to be in the same order as your list.files() command on your second line (the order of the names of the folders containing the ballgown data). Please rearrange the rows of pData to be in the or ...
written 5 weeks ago by Alyssa Frazee150
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Answer: A: How to simulate a count matrix using Polyester
... Yes, you can use a count matrix as input for polyester! Please see the "Simulating Reads" section of the vignette (subsection = "simulate_experiment_countmat example", which is available in the package vignette or at https://github.com/alyssafrazee/polyester#simulate_experiment_countmat-example. ?si ...
written 10 weeks ago by Alyssa Frazee150
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Answer: A: Handling both technical and biological replicates in Ballgown
... Hey Julian, the issue isn't that genes need to be excluded. If you get the "system is computationally singular" error, it means that one of your adjustvars" is perfectly correlated with either another adjustvar or the "covariate" variable (you can see this in the pData -- if there's any combination ...
written 12 weeks ago by Alyssa Frazee150
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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 3 months ago by Alyssa Frazee150
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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 3 months ago by Alyssa Frazee150
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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 3 months ago by Alyssa Frazee150

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Scholar 23 months ago, created an answer that has been accepted. For A: polyester: adding noise to RNASeq counts?

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