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dose
•
reset
0
votes
9
replies
4.5k
views
GEOquery installation problem
DOSE
DOSE
14.8 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 21.2 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
1.6k
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
987
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
988
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
989
views
How to change the siez of lables in heatmap
software error
go
dose
heatplot
gseGo
5.3 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
731
views
Disease semantic similarity
DOSE
5.0 years ago
ahmettoprak42
• 0
0
votes
1
reply
153
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 17 days ago by
Guido Hooiveld
★ 3.9k • written 21 days ago by
Lucie
• 0
0
votes
0
replies
920
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
9.5 years ago
Guangchuang Yu
★ 1.2k
0
votes
0
replies
757
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
2.7k
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
991
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: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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