User: Alyssa Frazee

gravatar for Alyssa Frazee
Alyssa Frazee200
Reputation:
200
Status:
Trusted
Location:
San Francisco, CA, USA
Website:
http://alyssafrazee.com/
Twitter:
@acfrazee
Last seen:
1 month, 3 weeks ago
Joined:
4 years, 2 months ago
Email:
a************@gmail.com

Posts by Alyssa Frazee

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Ballgown differential expression by exon problem
... Hello! You are correct that the subset command does not work for exons or introns. It only works for transcripts, which is why you can only use the column names of the transcript expression matrix (and not the exon or intron matrix). To use stattest with a filtered exon or intron table, I suggest m ...
written 8 weeks ago by Alyssa Frazee200
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Comment: C: DESeq2 vs Ballgown results
... Ballgown was not really designed for *gene*-level differential expression analysis -- it was written specifically to do *isoform*-level DE. Using DESeq2 with FeatureCounts is a much better-supported operation if your main interests are in gene-level DE. Count-based models like those in DESeq2 are to ...
written 4 months ago by Alyssa Frazee200
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Answer: A: DESeq2 vs Ballgown results
... I am also biased :D and actually in this case I agree with Mike! For *gene*-level analysis, count-based models are probably the way to go. Ballgown and FPKM in general are not really needed or designed for gene-level analysis; their main purpose is *isoform*-level analysis (where count-based modelin ...
written 7 months ago by Alyssa Frazee200
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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 9 months ago by Alyssa Frazee200
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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 9 months ago by Alyssa Frazee200
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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 9 months ago by Alyssa Frazee200
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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 10 months ago by Alyssa Frazee200
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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 10 months ago by Alyssa Frazee200
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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 11 months ago by Alyssa Frazee200
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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 11 months ago by Alyssa Frazee200

Latest awards to Alyssa Frazee

Scholar 17 months ago, created an answer that has been accepted. For A: polyester: adding noise to RNASeq counts?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Ballgown vs (voom,edgeR,DESeq,limma)
Scholar 2.6 years ago, created an answer that has been accepted. For A: polyester: adding noise to RNASeq counts?

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