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Showing :
Ballgown
•
reset
5
votes
14
replies
7.4k
views
DESeq2 vs Ballgown results
ballgown
deseq2
6.1 years ago
CE
▴ 20
3
votes
5
replies
6.6k
views
Ballgown up and down regulated genes
ballgown
differential expression
updated 7.0 years ago by
kapeelc
• 0 • written 8.3 years ago by
psbpedrobarbosa
▴ 10
2
votes
8
replies
5.7k
views
StringTie + Ballgown: handling biological replicates
ballgown
stringtie
updated 7.2 years ago by
linda.boshans
• 0 • written 8.2 years ago by
bhawley1991
▴ 10
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
Alyssa Frazee
▴ 210 • written 7.6 years ago by
boyashuang
• 0
0
votes
8
replies
3.7k
views
The common error with ballgown has not been solved!
ballgown
software error
updated 7.2 years ago by
Jeff Leek
▴ 650 • written 7.2 years ago by
Sara
▴ 10
1
vote
7
replies
3.5k
views
How fold change is calculated in Ballgown?
ballgown
7.3 years ago
Ir
• 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
0
votes
1
reply
2.8k
views
Ballgown Error in file(file, "rt") : invalid 'description' argument
rna-seq
ballgown
updated 6.7 years ago by
Alyssa Frazee
▴ 210 • written 6.7 years ago by
vinayjrao
• 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
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 7.2 years ago by
linda.boshans
• 0
1
vote
5
replies
2.4k
views
Error in stattest function
R
rnaseq
Ballgown
updated 2.9 years ago by
muhammadharoon974
• 0 • written 6.3 years ago by
amy16
• 0
0
votes
2
replies
2.3k
views
HISAT-StringTie-Ballgown, order of biological replicates in script design
ballgown
rna-seq
updated 7.3 years ago by
Alyssa Frazee
▴ 210 • written 7.3 years ago by
Ir
• 0
0
votes
1
reply
2.1k
views
trying to use ballgown with Sailfish/Salmon pipeline
rnaseq
multi-mapped reads
ballgown
salmon
timecourse
8.8 years ago
friederike.mgh
• 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
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
3
replies
2.0k
views
Error in ball gown command
rnaseq
ballgown
differential gene expression
updated 7.4 years ago by
Jeff Leek
▴ 650 • written 7.4 years ago by
kritikamish99
▴ 10
0
votes
1
reply
1.9k
views
Ballgown with replicates and the adjustvars option
ballgown
rnaseq
differential gene expression
updated 6.5 years ago by
Alyssa Frazee
▴ 210 • written 6.7 years ago by
o.diogosilva
• 0
1
vote
3
replies
1.9k
views
limma regularization on Ballgown
ballgown
limma
updated 6.9 years ago by
Alyssa Frazee
▴ 210 • written 6.9 years ago by
rodri2006
▴ 10
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
2
replies
1.8k
views
I'm worried that I can't use "ballgown" well
ballgown
rnaseq
updated 7.5 years ago by
James W. MacDonald
65k • written 7.5 years ago by
noset2769
• 0
1
vote
7
replies
1.8k
views
Ballgown object construction error
ballgown
scan
error
package
6.9 years ago
spaque57
• 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
3
votes
3
replies
1.8k
views
Specifying a Default Model in Ballgown
ballgown
updated 8.9 years ago by
Alyssa Frazee
▴ 210 • written 8.9 years ago by
andrea.hodgins.davis
• 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
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
4
replies
1.8k
views
Results with very few genes with qval <0.05
ballgown
updated 7.1 years ago by
aiwa
• 0 • written 7.2 years ago by
jdchc
• 0
0
votes
4
replies
1.8k
views
Ballgown from StringTie results transcripts which are not expressed in both conditions as Differentially expressed ones
ballgown
stringtie
updated 7.8 years ago by
Jeff Leek
▴ 650 • written 7.8 years ago by
alva.james
• 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
1
reply
1.7k
views
P value <0.05 and Q values~ 1
ballgown
updated 6.9 years ago by
Jeff Leek
▴ 650 • written 6.9 years ago by
akilabioinfo
• 0
2
votes
4
replies
1.7k
views
error reading ballgown object
R
ballgown
6.3 years ago
l.j.leach
• 0
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
Gordon Smyth
50k • written 5.3 years ago by
IRAIA.MAIALEN
• 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
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
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 22 months ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
lakshmi9c
• 0
0
votes
2
replies
1.4k
views
IRanges error loading rsem data into ballgown
ballgown
updated 7.2 years ago by
Jeff Leek
▴ 650 • written 7.2 years ago by
jchenpku
• 0
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
Alyssa Frazee
▴ 210 • written 7.6 years ago by
jcalis
▴ 10
1
vote
1
reply
1.4k
views
RNA-seq for DGE
stringtie
illumina
hisat2
ballgown
updated 6.5 years ago by
k.vitting.seerup
▴ 120 • written 6.5 years ago by
amy16
• 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
James W. MacDonald
65k • written 6.2 years ago by
ag1805x
▴ 80
0
votes
0
replies
1.4k
views
Ballgown data processing error
Ballgown
Stringtie
DEG
rnaseq
6.0 years ago
vharshavardhanan
• 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
0
replies
1.3k
views
Please help with ballgown problem
ballgown
differential expression
7.2 years ago
Sara
▴ 10
1
vote
0
replies
1.3k
views
covariate vs adjustvars
ballgown
rnaseq
differential gene expression
tuxedo
5.8 years ago
justinjj
▴ 10
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
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
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
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
2
votes
2
replies
1.0k
views
Ballgown Custom Model Question
ballgown
rnaseq
updated 7.7 years ago by
Jeff Leek
▴ 650 • written 7.7 years ago by
daniel.gaston
• 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
James W. MacDonald
65k • written 6.0 years ago by
ryanding2003
• 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
2
votes
0
replies
990
views
p-values, q-values, duplicated entries in output - ballgown
ballgown
rna-seq
q value
r
6.6 years ago
mkhasin
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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