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DOSE
•
reset
0
votes
9
replies
4.5k
views
GEOquery installation problem
DOSE
DOSE
14.7 years ago
zhihua zhang
▴ 50
2
votes
6
replies
3.1k
views
leading edge analysis clusterProfiler DOSE custom GSEA
clusterprofiler
DOSE
GSEA_internal
USER_DATA
leading edge Analysis
7.6 years ago
Riba Michela
▴ 90
0
votes
5
replies
1.3k
views
the result of bioconductor not agree with MAS
DOSE
DOSE
updated 21.1 years ago by
"Hüsing, Johannes"
▴ 60 • written 21.2 years ago by
Lang Chen
▴ 100
2
votes
5
replies
1.8k
views
Need help setting up DESeq2 complex model for multi-dose experiment
deseq2
multiple time points
dose
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
stwestreich
• 0
0
votes
5
replies
3.0k
views
Finding genes with significant linear regression or trend
Microarray
Regression
Cancer
limma
DOSE
Microarray
Regression
Cancer
limma
DOSE
updated 16.0 years ago by
Ana Conesa
▴ 340 • written 16.0 years ago by
Daniel Brewer
★ 1.9k
0
votes
4
replies
1.5k
views
microarray analysis of a dose response * strain experiment
affy
DOSE
BRAIN
affy
DOSE
BRAIN
updated 17.5 years ago by
Sean Davis
21k • written 17.5 years ago by
Kimpel, Mark W
▴ 890
4
votes
4
replies
4.2k
views
Clarifications on p-values in enrichResult objects
clusterProfiler
reactomepa
dose
updated 18 months ago by
12133067
• 0 • written 7.7 years ago by
enricoferrero
▴ 660
0
votes
4
replies
1.6k
views
GEO annotation
Annotation
DOSE
Annotation
DOSE
updated 15.9 years ago by
Marc Carlson
★ 7.2k • written 15.9 years ago by
Roumyana Yordanova
▴ 110
1
vote
4
replies
3.1k
views
gseDO function input
DOSE
clusterprofiler
updated 6.7 years ago by
Guangchuang Yu
★ 1.2k • written 6.7 years ago by
xr2120
• 0
0
votes
3
replies
1.8k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO
clusterProfiler
DOSE
GO
clusterProfiler
DOSE
updated 10.8 years ago by
Dan Tenenbaum
★ 8.2k • written 10.8 years ago by
Guest User
★ 13k
4
votes
3
replies
1.8k
views
BiocParallel: object export issue
BiocParallel
DOSE
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
Guido Hooiveld
★ 3.9k
0
votes
3
replies
1.2k
views
when do linear models work?
DOSE
DOSE
20.2 years ago
Arne.Muller@aventis.com
▴ 620
0
votes
3
replies
3.6k
views
Unable to generate a dotplot to view the enrichment analysis results (clusterProfiler/ enrichplot)
clusterProfiler
enrichplot
clusterpro
doseR
dose
updated 21 months ago by
Guido Hooiveld
★ 3.9k • written 22 months ago by
rama
▴ 10
0
votes
3
replies
1.2k
views
Failed to install 'DOSE' package. Win10, 'single candle'
DOSE
package installation
windows10
6.8 years ago
Yisong Zhen
▴ 200
1
vote
3
replies
1.6k
views
Subset of genes can find a term but whole set cannot
biomart
dose
updated 6.9 years ago by
James W. MacDonald
65k • written 6.9 years ago by
ankita.mandal28529
• 0
2
votes
2
replies
3.5k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE
clusterprofiler
annotation
gene ontology
gene set enrichment
updated 6.5 years ago by
Guangchuang Yu
★ 1.2k • written 6.5 years ago by
kirannbishwa01
▴ 10
0
votes
2
replies
1.3k
views
about limma linear models
Microarray
limma
DOSE
Microarray
limma
DOSE
updated 13.0 years ago by
sense_0109
▴ 40 • written 13.0 years ago by
Gordon Smyth
50k
0
votes
2
replies
1.8k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation
cdf
probe
affy
oligo
xps
DOSE
Annotation
cdf
probe
affy
oligo
xps
DOSE
updated 13.4 years ago by
Benilton Carvalho
★ 4.3k • written 13.4 years ago by
branislav misovic
▴ 120
0
votes
2
replies
2.0k
views
DO.db is missing after repeated installations-ReactomePA-ClusterProfiler-DOSE
software error
reactomePA
DOSE
DO.db
there is no package called ‘DO.db’
updated 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
goodwinjinesh
• 0
1
vote
2
replies
2.5k
views
Regression using LIMMA
affy
limma
DOSE
affy
limma
DOSE
updated 13.5 years ago by
Naomi Altman
★ 6.0k • written 13.5 years ago by
fire1976 wyoming
▴ 380
0
votes
2
replies
1.5k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE
ReactomePA
enrichMap
enrichPathway
updated 6.3 years ago by
Guangchuang Yu
★ 1.2k • written 6.3 years ago by
jan.soderman
• 0
0
votes
2
replies
1.8k
views
question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray
DOSE
Microarray
DOSE
updated 10.4 years ago by
Pekka Kohonen
▴ 190 • written 10.4 years ago by
Guest User
★ 13k
0
votes
2
replies
1.5k
views
FW: PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation
cdf
probe
affy
oligo
xps
DOSE
Annotation
cdf
probe
affy
oligo
xps
DOSE
updated 13.4 years ago by
branislav misovic
▴ 120 • written 13.4 years ago by
Ramil Nurtdinov
▴ 10
1
vote
2
replies
5.5k
views
ClusterProfiler DotPlot Vs Ridgeplot
clusterProfiler
DOSE
updated 16 months ago by
Nick O
• 0 • written 20 months ago by
ummscr
• 0
0
votes
1
reply
1.5k
views
Re: Limma: M value in toptable
limma
DOSE
limma
DOSE
updated 19.2 years ago by
Hua Weng
▴ 60 • written 19.2 years ago by
Gordon Smyth
50k
0
votes
1
reply
2.1k
views
Question on unbalanced paired design
Microarray
Normalization
GO
limma
DOSE
Microarray
Normalization
GO
limma
DOSE
updated 11.1 years ago by
Ryan C. Thompson
★ 7.9k • written 11.1 years ago by
Sandhya Pemmasani Kiran
▴ 40
1
vote
1
reply
1.6k
views
ReactomePA viewPathway DE node and legend colour
DOSE
ReactomePA
7.3 years ago
Kajus Baidžajevas
▴ 10
0
votes
1
reply
984
views
methodological question
DOSE
DOSE
updated 21.0 years ago by
Eric Blalock
▴ 250 • written 21.0 years ago by
Phguardiol@aol.com
▴ 720
0
votes
1
reply
685
views
Program No Responding
DOSE
DOSE
updated 21.0 years ago by
A.J. Rossini
▴ 810 • written 21.0 years ago by
Lang Chen
▴ 100
0
votes
1
reply
987
views
programming problem: running many ANOVAs
DOSE
DOSE
updated 20.0 years ago by
Francois Collin
▴ 130 • written 20.0 years ago by
Arne.Muller@aventis.com
▴ 620
0
votes
1
reply
1.3k
views
unbalanced design
limma
DOSE
limma
DOSE
updated 19.4 years ago by
Gordon Smyth
50k • written 19.4 years ago by
Arne.Muller@aventis.com
▴ 620
0
votes
1
reply
1.2k
views
normalizaton between studies
Normalization
vsn
DOSE
Normalization
vsn
DOSE
updated 19.4 years ago by
Anja.von.Heydebreck@merck.de
▴ 10 • written 19.4 years ago by
Arne.Muller@aventis.com
▴ 620
0
votes
1
reply
2.1k
views
Dose-Response: Regressiion and ANOVA
Regression
DOSE
Regression
DOSE
updated 19.3 years ago by
Liaw, Andy
▴ 360 • written 19.3 years ago by
Arne.Muller@aventis.com
▴ 620
0
votes
1
reply
1.2k
views
limma: writing down the matrix in an almost (?) factorial design experiment
Microarray
DOSE
Microarray
DOSE
14.2 years ago
Massimo Pinto
▴ 390
0
votes
1
reply
1.5k
views
LIMMA: donor effect
Microarray
limma
DOSE
Microarray
limma
DOSE
updated 13.0 years ago by
fire1976 wyoming
▴ 380 • written 13.0 years ago by
Gordon Smyth
50k
0
votes
1
reply
1.4k
views
strange log2FoldChange estimates
RNASeq
DOSE
DESeq2
RNASeq
DOSE
DESeq2
9.7 years ago
Shi, Tao
▴ 720
1
vote
1
reply
1.6k
views
Treatment dose in treatment-control RNA-seq
deseq2
edger
dose
rna-seq
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
JacobK
• 0
0
votes
1
reply
988
views
How to change the siez of lables in heatmap
software error
go
dose
heatplot
gseGo
5.2 years ago
aboumarshal
• 0
1
vote
1
reply
1.2k
views
dotplot in DOSE
compilation error
DOSE
6.0 years ago
alper.kucukural
▴ 10
0
votes
1
reply
730
views
Disease semantic similarity
DOSE
5.0 years ago
ahmettoprak42
• 0
0
votes
1
reply
139
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 14 days ago by
Guido Hooiveld
★ 3.9k • written 17 days ago by
Lucie
• 0
0
votes
0
replies
919
views
Re: Classification question(Tom R. Fahland)
Classification
DOSE
Classification
DOSE
20.0 years ago
Tarca Adi Laurentiu
▴ 100
0
votes
0
replies
1.2k
views
Re: OpenPBS
webbioc
DOSE
webbioc
DOSE
20.5 years ago
Colin A. Smith
▴ 220
0
votes
0
replies
1.7k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment
genesetenrichment
dose
gosemsim
9.4 years ago
Guangchuang Yu
★ 1.2k
0
votes
0
replies
753
views
Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE
hypeR
goTools
GOstats
topGO
3.4 years ago
Madza Farias-Virgens
• 0
0
votes
0
replies
2.6k
views
Modifying the legend in cnetplot function
clusterProfiler
DOSE
8.4 years ago
Vinicius Henrique da Silva
▴ 40
0
votes
0
replies
1.6k
views
RMA normalization,which samples should be normalized together
Normalization
probe
affy
limma
gcrma
DOSE
Normalization
probe
affy
limma
gcrma
DOSE
19.2 years ago
Dipl.-Ing. Johannes Rainer
▴ 430
0
votes
0
replies
1.1k
views
Friedman test
DOSE
DOSE
19.7 years ago
Arne.Muller@aventis.com
▴ 620
0
votes
0
replies
1.5k
views
Anova with ratios
affy
DOSE
affy
DOSE
19.9 years ago
Arne.Muller@aventis.com
▴ 620
0
votes
0
replies
987
views
Probe level analysis
probe
limma
DOSE
probe
limma
DOSE
20.0 years ago
Arne.Muller@aventis.com
▴ 620
50 results • Page
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Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
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