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Showing :
ballgown
•
reset
0
votes
4
replies
373
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
12 weeks ago
candacenewcome
• 0
1
vote
2
replies
409
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2
DGEanalysis
ballgown
Ballgown
DiseasedvsNormal
9 months ago
Bushra
• 0
0
votes
1
reply
951
views
is.null(pData) | class(pData) == "data.frame" is not TRUE
ballgown
updated 2.6 years ago by
Hervé Pagès
16k • written 2.6 years ago by
merden1603
• 0
1
vote
5
replies
2.4k
views
Error in stattest function
R
rnaseq
Ballgown
updated 2.9 years ago by
muhammadharoon974
• 0 • written 6.2 years ago by
amy16
• 0
0
votes
1
reply
971
views
Ballgown stattest: Why do p-values change when changing filtration?
ballgown
updated 3.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 3.5 years ago by
katrinegraversen
• 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
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
Alyssa Frazee
▴ 210 • written 3.6 years ago by
pushgct
• 0
0
votes
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 22 months ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
lakshmi9c
• 0
1
vote
2
replies
869
views
Regularization of ballgown object on Limma
limma
ballgown
RNA-seq
4.2 years ago
komuracom16
• 0
0
votes
0
replies
791
views
Is the ballgownrsem function still supported?
ballgown
rsem
iranges
4.4 years ago • updated 4.3 years ago
YH
• 0
0
votes
0
replies
646
views
ballgown -- how is statistical test performed
ballgown
rna-seq
4.6 years ago
michael
• 0
0
votes
0
replies
600
views
ballgown: how to test for DE for my experimental setup
ballgown
rna-seq
4.6 years ago
michael
• 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
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
Alyssa Frazee
▴ 210 • written 5.3 years ago by
aaubry89
• 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
Gordon Smyth
50k • written 5.3 years ago by
IRAIA.MAIALEN
• 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
1
reply
2.1k
views
Can not install packages
ballgown
genefilter
RskittleBrewer
updated 5.5 years ago by
Mike Smith
★ 6.5k • written 5.5 years ago by
Mithil Gaikwad
• 0
0
votes
0
replies
818
views
Aboutfc value in stringtie hisat2 ballgown pipeline
ballgown r
ballgown
5.5 years ago
viv333chavan
• 0
0
votes
1
reply
777
views
Understanding the output from Ballgown for DE
changes
ballgown
5.6 years ago
amy16
• 0
0
votes
0
replies
777
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
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
James W. MacDonald
65k • written 5.6 years ago by
dualeahmed
• 0
0
votes
2
replies
930
views
Including batch effects in the differential expression of gene analysis
ballgown
new tuxedo pipleine
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
amy16
• 0
1
vote
1
reply
768
views
ballgown bamfiles vector
ballgown
5.7 years ago
jac1318
• 0
0
votes
1
reply
772
views
Ballgown Plotmeans problem
ballgown
5.7 years ago
new_user
• 0
0
votes
0
replies
961
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
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
1
reply
981
views
Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
ballgown
5.8 years ago
harris
• 0
1
vote
0
replies
1.2k
views
covariate vs adjustvars
ballgown
rnaseq
differential gene expression
tuxedo
5.8 years ago
justinjj
▴ 10
0
votes
0
replies
976
views
pair wise ballgown
ballgown
differential expression
5.8 years ago
zoe.ward
• 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
James W. MacDonald
65k • written 5.8 years ago by
khill33
• 0
0
votes
1
reply
859
views
Ballgown for differential expressed genes
ballgown
5.9 years ago
marasodi
• 0
0
votes
2
replies
1.0k
views
Ballgown for differential expressed genes
ballgown
updated 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
marasodi
• 0
1
vote
2
replies
987
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
James W. MacDonald
65k • written 6.0 years ago by
ryanding2003
• 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
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
712
views
pairwise comparison with ballgown
ballgown
6.0 years ago
behnam.derakhshani
• 0
0
votes
0
replies
828
views
Model problem using ballgown
ballgown
linear models
6.0 years ago
Yong Li
▴ 50
0
votes
1
reply
898
views
ballgown time course design and command confirmation
ballgown
stattest
multiple time points
6.0 years ago
yadongxue
• 0
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error
illumina
DEG
ballgown
tuxedo
updated 6.1 years ago by
James W. MacDonald
65k • written 6.1 years ago by
amy16
• 0
0
votes
0
replies
731
views
Ballgown data read error
ballgown
software error
6.1 years ago
amy16
• 0
5
votes
14
replies
7.4k
views
DESeq2 vs Ballgown results
ballgown
deseq2
6.1 years ago
CE
▴ 20
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
James W. MacDonald
65k • written 6.1 years ago by
ag1805x
▴ 80
2
votes
4
replies
1.7k
views
error reading ballgown object
R
ballgown
6.2 years ago
l.j.leach
• 0
0
votes
0
replies
802
views
Subset functionin R
R
ballgown
rnaseq
6.2 years ago
amy16
• 0
0
votes
0
replies
819
views
Accessing the assembly data-output
R
rnaseq
ballgown
6.2 years ago
amy16
• 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
importantrubbish
• 0 • written 6.7 years ago by
fubeide
• 0
1
vote
3
replies
2.6k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 6.3 years ago by
Alyssa Frazee
▴ 210 • written 6.3 years ago by
rachael.detar
▴ 10
1
vote
2
replies
1.5k
views
Error in reading ballgown object
R
ballgown
updated 6.3 years ago by
Alyssa Frazee
▴ 210 • written 6.3 years ago by
amy16
• 0
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
Alyssa Frazee
▴ 210 • written 7.1 years ago by
linda.boshans
• 0
50 results • Page
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Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Are you commenting on the OP's question, or adding a different question? If the latter, please start a new post rather than piggybacking on…
Answer: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Use `bquote`. See section 4.6 in [the vignette][1]. [1]: https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/in…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
SamGG
▴ 350
I was thinking about removing unwanted variations at the sample level (ie a transformation shared across genes) not at the gene level. Corr…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
That's an assumption used for normalization of a sample, not an assumption you can use for an individual model. We always normalize to atte…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
SamGG
▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Votes
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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