Showing : Ballgown • reset
5
votes
14
replies
7.4k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.1 years ago CE ▴ 20
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
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
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
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
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
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
2
votes
0
replies
982
views
p-values, q-values, duplicated entries in output - ballgown
ballgown rna-seq q value r
6.6 years ago mkhasin ▴ 20
2
votes
4
replies
1.7k
views
error reading ballgown object
R ballgown
6.2 years ago l.j.leach • 0
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
1
vote
2
replies
400
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
9 months ago Bushra • 0
1
vote
2
replies
867
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.2 years ago komuracom16 • 0
1
vote
2
replies
983
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
1
vote
7
replies
3.5k
views
How fold change is calculated in Ballgown?
ballgown
7.3 years ago Ir • 0
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
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
1
vote
0
replies
1.2k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
5.8 years ago justinjj ▴ 10
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
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
1
vote
1
reply
767
views
ballgown bamfiles vector
ballgown
5.7 years ago jac1318 • 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
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
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
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
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
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
0
votes
1
reply
945
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
0
votes
0
replies
975
views
pair wise ballgown
ballgown differential expression
5.8 years ago zoe.ward • 0
0
votes
1
reply
978
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
5.8 years ago harris • 0
0
votes
0
replies
956
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
1
reply
770
views
Ballgown Plotmeans problem
ballgown
5.7 years ago new_user • 0
0
votes
3
replies
1.5k
views
Ballgown differential expression by exon problem
ballgown
5.6 years ago new_user • 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
2
replies
929
views
Including batch effects in the differential expression of gene analysis
ballgown new tuxedo pipleine
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
0
replies
774
views
R script to fix the error in dataframe when using ballgown for differentially expression analysis
r ballgown code error
5.6 years ago amy16 • 0
0
votes
1
reply
773
views
Understanding the output from Ballgown for DE
changes ballgown
5.5 years ago amy16 • 0
0
votes
0
replies
817
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
5.5 years ago viv333chavan • 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
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
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
0
replies
598
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
4.6 years ago michael • 0
0
votes
0
replies
642
views
ballgown -- how is statistical test performed
ballgown rna-seq
4.6 years ago michael • 0
0
votes
0
replies
787
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
4.3 years ago YH • 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
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
0
votes
0
replies
1.3k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
3.5 years ago ra711 • 0
0
votes
1
reply
969
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 3.5 years ago by ★ 1.0k • written 3.5 years ago by • 0
0
votes
1
reply
948
views
is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 2.6 years ago by 16k • written 2.6 years ago by • 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
4
replies
369
views
Ballgown error in scan for c.tab files
ballgown RNASeq
11 weeks ago candacenewcome • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
I don't really have any additional suggestion here.
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Dear Michael, I tried all three ways (the orIginal, increasing the number of required samples,and subsetting (the countdata and metadata be…
Comment: DESeq2 - dispersion estimation when there is none by Michael Love 41k
The red line does assume that shape but the fact the black points show that pattern is discussed in the 2014 paper. > Some caution is warr…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
Comment: Methylation Analysis experiment design using Limma by hortense96 • 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Votes
DESeq2: How to find out how well the model fits the data?
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Awards • All
Scholar to Michael Love 41k
Popular Question to shepherl 3.8k
Scholar to Gordon Smyth 50k
Popular Question to taur.vil • 0
Teacher to Yuan Tian ▴ 280
Locations • All
United Kingdom, 2 minutes ago
United States, 3 minutes ago
EMBL Heidelberg, 5 minutes ago
United Kingdom, 6 minutes ago
France, 9 minutes ago
Traffic: 907 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