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 8.9 years ago by ▴ 210 • written 8.9 years ago by • 0
3
votes
5
replies
6.6k
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 7.2 years ago by • 0 • written 8.2 years ago by ▴ 10
2
votes
2
replies
1.6k
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
989
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
6.3 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 7.6 years ago by • 0
1
vote
2
replies
419
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
9 months ago Bushra • 0
1
vote
2
replies
882
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.3 years ago komuracom16 • 0
1
vote
2
replies
1000
views
RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 6.0 years ago by 65k • written 6.0 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 6.5 years ago by ▴ 120 • written 6.5 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
1
vote
0
replies
1.3k
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
776
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 6.3 years ago by • 0
1
vote
1
reply
1.4k
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 5.3 years ago by ▴ 210 • written 5.3 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 spaque57 • 0
0
votes
1
reply
951
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
0
replies
989
views
pair wise ballgown
ballgown differential expression
5.9 years ago zoe.ward • 0
0
votes
1
reply
991
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
966
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
779
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
5.7 years ago • updated 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
936
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
782
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
785
views
Understanding the output from Ballgown for DE
changes ballgown
5.6 years ago amy16 • 0
0
votes
0
replies
826
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
5.5 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
5.1 years ago fatimarasool135 • 0
0
votes
0
replies
605
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
4.6 years ago michael • 0
0
votes
0
replies
653
views
ballgown -- how is statistical test performed
ballgown rna-seq
4.6 years ago michael • 0
0
votes
0
replies
799
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
4.4 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 3.8 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
3.6 years ago ra711 • 0
0
votes
1
reply
980
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
964
views
is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 2.7 years ago by 16k • written 2.7 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
393
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Votes
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
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