## User: Alyssa Frazee

Alyssa Frazee210
Reputation:
210
Status:
Trusted
Location:
San Francisco, CA, USA
Website:
http://alyssafrazee.com/
@acfrazee
Last seen:
6 days, 10 hours ago
Joined:
5 years ago
Email:
a************@gmail.com

#### Posts by Alyssa Frazee

<prev • 38 results • page 1 of 4 • next >
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... Hi Pooja, ballgown has a subset method built in that operates directly on the objects: https://rdrr.io/bioc/ballgown/man/subset.html You can also find these docs by doing ?subset in R after loading up the ballgown library. Good luck! ...
written 6 days ago by Alyssa Frazee210
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... The error seen here is "is.null(pData) | class(pData) == "data.frame" are not all TRUE. It looks like the command you ran below (whether phenodata\$ids == list.files("ballgown")) is a step ahead of what's going wrong and is not actually addressing the class of phenodata. I'd evaluate is.null(phenodat ...
written 7 months ago by Alyssa Frazee210
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367
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... 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 12 months ago by Alyssa Frazee210
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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 14 months ago by Alyssa Frazee210
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... 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 18 months ago by Alyssa Frazee210
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515
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... 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 19 months ago by Alyssa Frazee210
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575
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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 19 months ago by Alyssa Frazee210
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575
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... 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 19 months ago by Alyssa Frazee210
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668
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... 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 20 months ago by Alyssa Frazee210
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... 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 20 months ago by Alyssa Frazee210

#### Latest awards to Alyssa Frazee

Scholar 2.3 years ago, created an answer that has been accepted. For A: polyester: adding noise to RNASeq counts?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Ballgown vs (voom,edgeR,DESeq,limma)
Scholar 3.5 years ago, created an answer that has been accepted. For A: polyester: adding noise to RNASeq counts?

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