Showing : Ballgown • reset
5
votes
14
replies
7.4k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.1 years ago CE ▴ 20
3
votes
5
replies
6.5k
views
Ballgown up and down regulated genes
ballgown differential expression
updated 7.0 years ago by • 0 • written 8.3 years ago by ▴ 10
2
votes
8
replies
5.7k
views
StringTie + Ballgown: handling biological replicates
ballgown stringtie
updated 7.1 years ago by • 0 • written 8.1 years ago by ▴ 10
2
votes
5
replies
4.0k
views
processing data with 2 rep or one replicate by ballgown
ballgown differential gene expression
updated 7.5 years ago by ▴ 210 • written 7.5 years ago by • 0
0
votes
8
replies
3.7k
views
The common error with ballgown has not been solved!
ballgown software error
updated 7.2 years ago by ▴ 650 • written 7.2 years ago by ▴ 10
1
vote
7
replies
3.5k
views
How fold change is calculated in Ballgown?
ballgown
7.3 years ago Ir • 0
2
votes
7
replies
3.1k
views
ballgown custom models
ballgown linear model model matrix custom model
8.1 years ago • updated 8.0 years ago sbcn ▴ 80
0
votes
1
reply
2.8k
views
Ballgown Error in file(file, "rt") : invalid 'description' argument
rna-seq ballgown
updated 6.6 years ago by ▴ 210 • written 6.6 years ago by • 0
1
vote
3
replies
2.6k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 6.3 years ago by ▴ 210 • written 6.3 years ago by ▴ 10
0
votes
7
replies
2.5k
views
Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 6.4 years ago by ▴ 210 • written 7.1 years ago by • 0
1
vote
5
replies
2.4k
views
Error in stattest function
R rnaseq Ballgown
updated 2.9 years ago by • 0 • written 6.2 years ago by • 0
0
votes
2
replies
2.2k
views
HISAT-StringTie-Ballgown, order of biological replicates in script design
ballgown rna-seq
updated 7.3 years ago by ▴ 210 • written 7.3 years ago by • 0
0
votes
1
reply
2.1k
views
trying to use ballgown with Sailfish/Salmon pipeline
rnaseq multi-mapped reads ballgown salmon timecourse
8.8 years ago friederike.mgh • 0
0
votes
1
reply
2.1k
views
Can not install packages
ballgown genefilter RskittleBrewer
updated 5.5 years ago by ★ 6.5k • written 5.5 years ago by • 0
1
vote
0
replies
2.0k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
5.8 years ago kicheol.kim • 0
0
votes
3
replies
2.0k
views
Error in ball gown command
rnaseq ballgown differential gene expression
updated 7.4 years ago by ▴ 650 • written 7.4 years ago by ▴ 10
0
votes
1
reply
1.9k
views
Ballgown with replicates and the adjustvars option
ballgown rnaseq differential gene expression
updated 6.5 years ago by ▴ 210 • written 6.7 years ago by • 0
1
vote
3
replies
1.9k
views
limma regularization on Ballgown
ballgown limma
updated 6.9 years ago by ▴ 210 • written 6.9 years ago by ▴ 10
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.0 years ago by 65k • written 6.1 years ago by • 0
0
votes
2
replies
1.8k
views
I'm worried that I can't use "ballgown" well
ballgown rnaseq
updated 7.5 years ago by 65k • written 7.5 years ago by • 0
0
votes
0
replies
1.8k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
6.2 years ago • updated 6.0 years ago Nancy ▴ 10
1
vote
7
replies
1.8k
views
Ballgown object construction error
ballgown scan error package
6.9 years ago • updated 6.8 years ago spaque57 • 0
3
votes
3
replies
1.8k
views
Specifying a Default Model in Ballgown
ballgown
updated 8.8 years ago by ▴ 210 • written 8.8 years ago by • 0
0
votes
1
reply
1.8k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
3
replies
1.8k
views
error in filtering genes with rowVars(gexpr(bg_chrX)) >1
genefilter ballgown
updated 6.3 years ago by • 0 • written 6.7 years ago by • 0
0
votes
4
replies
1.8k
views
Ballgown from StringTie results transcripts which are not expressed in both conditions as Differentially expressed ones
ballgown stringtie
updated 7.8 years ago by ▴ 650 • written 7.8 years ago by • 0
0
votes
4
replies
1.8k
views
Results with very few genes with qval <0.05
ballgown
updated 7.1 years ago by • 0 • written 7.1 years ago by • 0
0
votes
0
replies
1.7k
views
Error in contrasts<-(tmp, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels
software error ballgown rstudio R stattest
5.0 years ago fatimarasool135 • 0
0
votes
1
reply
1.7k
views
P value <0.05 and Q values~ 1
ballgown
updated 6.9 years ago by ▴ 650 • written 6.9 years ago by • 0
2
votes
4
replies
1.7k
views
error reading ballgown object
R ballgown
6.2 years ago l.j.leach • 0
2
votes
2
replies
1.5k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 5.3 years ago by 50k • written 5.3 years ago by • 0
0
votes
3
replies
1.5k
views
Ballgown differential expression by exon problem
ballgown
5.6 years ago new_user • 0
1
vote
2
replies
1.5k
views
Error in reading ballgown object
R ballgown
updated 6.3 years ago by ▴ 210 • written 6.3 years ago by • 0
0
votes
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 22 months ago by ★ 3.9k • written 3.7 years ago by • 0
0
votes
2
replies
1.4k
views
IRanges error loading rsem data into ballgown
ballgown
updated 7.2 years ago by ▴ 650 • written 7.2 years ago by • 0
1
vote
3
replies
1.4k
views
Interaction term analysis using ballgown
ballgown stringtie voom limma differential gene expression rnaseq
updated 7.6 years ago by ▴ 210 • written 7.6 years ago by ▴ 10
1
vote
1
reply
1.4k
views
RNA-seq for DGE
stringtie illumina hisat2 ballgown
updated 6.4 years ago by ▴ 120 • written 6.4 years ago by • 0
1
vote
1
reply
1.3k
views
What is the exact formula for the calculation of Fold Change (FC), p-val and q-val in Ballgown stattest?
ballgown stattest fold change
updated 6.1 years ago by 65k • written 6.1 years ago by ▴ 80
0
votes
0
replies
1.3k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.0 years ago vharshavardhanan • 0
0
votes
0
replies
1.3k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
3.6 years ago ra711 • 0
0
votes
0
replies
1.3k
views
Please help with ballgown problem
ballgown differential expression
7.2 years ago Sara ▴ 10
1
vote
0
replies
1.2k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
5.8 years ago justinjj ▴ 10
0
votes
1
reply
1.2k
views
Error loading sample and control data using Ballgown due to different i_id in i_data.ctab
ballgown i_data.ctab differential gene expression
updated 3.6 years ago by ▴ 210 • written 3.6 years ago by • 0
1
vote
2
replies
1.1k
views
Ballgown Error .null(pData) | class(pData) == "data.frame" are not all TRUE
software error ballgown
updated 5.2 years ago by ▴ 210 • written 5.2 years ago by • 0
0
votes
0
replies
1.1k
views
Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
5.4 years ago Mithil Gaikwad • 0
2
votes
2
replies
1.0k
views
Ballgown Custom Model Question
ballgown rnaseq
updated 7.7 years ago by ▴ 650 • written 7.7 years ago by • 0
0
votes
2
replies
1.0k
views
Ballgown for differential expressed genes
ballgown
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
1
vote
2
replies
984
views
RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
2
votes
0
replies
983
views
p-values, q-values, duplicated entries in output - ballgown
ballgown rna-seq q value r
6.6 years ago mkhasin ▴ 20
0
votes
1
reply
980
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
5.8 years ago harris • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
Awards • All
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Popular Question to Bine ▴ 40
Locations • All
The city by the bay, 3 minutes ago
France, 8 minutes ago
China, 12 minutes ago
India, 19 minutes ago
San Diego, 57 minutes ago
Traffic: 712 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6