Showing : ballgown • reset
0
votes
4
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747
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Ballgown error in scan for c.tab files
ballgown RNASeq
11 months ago candacenewcome • 0
1
vote
2
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665
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DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
17 months ago Bushra • 0
0
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1
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1.2k
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is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 3.3 years ago by 16k • written 3.3 years ago by • 0
1
vote
5
replies
2.7k
views
Error in stattest function
R rnaseq Ballgown
updated 3.6 years ago by • 0 • written 6.9 years ago by • 0
0
votes
1
reply
1.2k
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 4.2 years ago by ★ 1.1k • written 4.2 years ago by • 0
0
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0
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1.6k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
4.3 years ago ra711 • 0
0
votes
1
reply
1.4k
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 4.3 years ago by ▴ 210 • written 4.3 years ago by • 0
0
votes
3
replies
1.8k
views
StringTie output as Ballgown input
ballgown StringTie galaxy rnaseq
updated 2.5 years ago by ★ 4.0k • written 4.4 years ago by • 0
1
vote
2
replies
1.1k
views
Regularization of ballgown object on Limma
limma ballgown RNA-seq
4.9 years ago komuracom16 • 0
0
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0
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1.0k
views
Is the ballgownrsem function still supported?
ballgown rsem iranges
5.0 years ago YH • 0
0
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0
replies
790
views
ballgown -- how is statistical test performed
ballgown rna-seq
5.3 years ago michael • 0
0
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0
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793
views
ballgown: how to test for DE for my experimental setup
ballgown rna-seq
5.3 years ago michael • 0
0
votes
0
replies
2.1k
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
5.7 years ago fatimarasool135 • 0
1
vote
2
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1.4k
views
Ballgown Error .null(pData) | class(pData) == "data.frame" are not all TRUE
software error ballgown
updated 5.9 years ago by ▴ 210 • written 5.9 years ago by • 0
2
votes
2
replies
1.9k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 6.0 years ago by 52k • written 6.0 years ago by • 0
0
votes
0
replies
1.3k
views
Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
6.1 years ago Mithil Gaikwad • 0
0
votes
1
reply
2.3k
views
Can not install packages
ballgown genefilter RskittleBrewer
updated 6.2 years ago by ★ 6.6k • written 6.2 years ago by • 0
0
votes
0
replies
963
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r ballgown
6.2 years ago viv333chavan • 0
0
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1
reply
913
views
Understanding the output from Ballgown for DE
changes ballgown
6.2 years ago amy16 • 0
0
votes
0
replies
946
views
R script to fix the error in dataframe when using ballgown for differentially expression analysis
r ballgown code error
6.3 years ago amy16 • 0
0
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3
replies
1.8k
views
Ballgown differential expression by exon problem
ballgown
6.3 years ago new_user • 0
0
votes
1
reply
2.0k
views
Issue using ballgown
software error ballgown genomeinfodbdata genomeinfodb
updated 6.3 years ago by 67k • written 6.3 years ago by • 0
0
votes
2
replies
1.1k
views
Including batch effects in the differential expression of gene analysis
ballgown new tuxedo pipleine
updated 6.3 years ago by 67k • written 6.3 years ago by • 0
1
vote
1
reply
924
views
ballgown bamfiles vector
ballgown
6.4 years ago jac1318 • 0
0
votes
1
reply
923
views
Ballgown Plotmeans problem
ballgown
6.4 years ago new_user • 0
0
votes
0
replies
1.1k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.5 years ago kicheol.kim • 0
1
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0
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2.2k
views
IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
ballgown rsem iranges
6.5 years ago kicheol.kim • 0
0
votes
1
reply
1.1k
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
6.5 years ago harris • 0
1
vote
0
replies
1.4k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
6.5 years ago justinjj ▴ 10
0
votes
0
replies
1.2k
views
pair wise ballgown
ballgown differential expression
6.5 years ago zoe.ward • 0
0
votes
1
reply
1.1k
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 6.5 years ago by 67k • written 6.5 years ago by • 0
0
votes
1
reply
1.1k
views
Ballgown for differential expressed genes
ballgown
6.6 years ago marasodi • 0
0
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2
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1.2k
views
Ballgown for differential expressed genes
ballgown
updated 6.6 years ago by 67k • written 6.6 years ago by • 0
1
vote
2
replies
1.2k
views
RNA-Seq differential analysis with ballgown, getting more significantly deferentially expressed genes than significantly deferentially expressed tra…
ballgown
updated 6.6 years ago by 67k • written 6.6 years ago by • 0
0
votes
0
replies
2.1k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2 stringtie ballgown RNAseq
6.9 years ago • updated 6.7 years ago Nancy ▴ 10
0
votes
0
replies
1.5k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.7 years ago vharshavardhanan • 0
0
votes
0
replies
829
views
pairwise comparison with ballgown
ballgown
6.7 years ago behnam.derakhshani • 0
0
votes
0
replies
984
views
Model problem using ballgown
ballgown linear models
6.7 years ago Yong Li ▴ 50
0
votes
1
reply
1.1k
views
ballgown time course design and command confirmation
ballgown stattest multiple time points
6.7 years ago yadongxue • 0
0
votes
3
replies
2.1k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.7 years ago by 67k • written 6.8 years ago by • 0
0
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0
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839
views
Ballgown data read error
ballgown software error
6.8 years ago amy16 • 0
5
votes
14
replies
8.2k
views
DESeq2 vs Ballgown results
ballgown deseq2
6.8 years ago CE ▴ 20
1
vote
1
reply
1.6k
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 6.8 years ago by 67k • written 6.8 years ago by ▴ 80
2
votes
4
replies
1.9k
views
error reading ballgown object
R ballgown
6.9 years ago l.j.leach • 0
0
votes
0
replies
971
views
Subset functionin R
R ballgown rnaseq
6.9 years ago amy16 • 0
0
votes
0
replies
949
views
Accessing the assembly data-output
R rnaseq ballgown
6.9 years ago amy16 • 0
0
votes
3
replies
2.0k
views
error in filtering genes with rowVars(gexpr(bg_chrX)) >1
genefilter ballgown
updated 7.0 years ago by • 0 • written 7.4 years ago by • 0
1
vote
3
replies
3.0k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 7.0 years ago by ▴ 210 • written 7.0 years ago by ▴ 10
1
vote
2
replies
1.8k
views
Error in reading ballgown object
R ballgown
updated 7.0 years ago by ▴ 210 • written 7.0 years ago by • 0
0
votes
7
replies
2.9k
views
Handling both technical and biological replicates in Ballgown
ballgown biologicalreplicates technical replicates stringtie
updated 7.1 years ago by ▴ 210 • written 7.8 years ago by • 0
50 results • Page 1 of 1
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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
Sorry, I cannot follow what you're saying. The two code sequences you show look to be exactly the same.
Answer: Mean variance curve troubleshoot filtering by Gordon Smyth 52k
You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies. However, the main problem wi…
Comment: How do I fix an odd voom plot in a combined dataset? by Gordon Smyth 52k
The fact that you have partial NA coefficients indicates that your merged dataset consists in good part of NAs for a very large number of g…
Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0
Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…
Votes
Answer: How do I fix an odd voom plot in a combined dataset?
Answer: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
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