Showing : ballgown • reset
5
votes
14
replies
7.4k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.2 years ago • updated 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
992
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
422
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
9 months ago Bushra • 0
1
vote
2
replies
889
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.3 years ago komuracom16 • 0
1
vote
2
replies
1.0k
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
5.9 years ago • updated 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
777
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 6.2 years ago by 65k • written 6.2 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
952
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
992
views
pair wise ballgown
ballgown differential expression
5.9 years ago zoe.ward • 0
0
votes
1
reply
992
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
968
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
781
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
938
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
783
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
828
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
606
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
4.6 years ago michael • 0
0
votes
0
replies
654
views
ballgown -- how is statistical test performed
ballgown rna-seq
4.6 years ago michael • 0
0
votes
0
replies
803
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 3.7 years ago by ▴ 210 • written 3.7 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
982
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
966
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
402
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
50 results • Page 1 of 1
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Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
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