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Votes
0
votes
17
replies
3.2k
views
Finding DMRs using dmrFinder in bsseq
bsseq R package
7.0 years ago
Maria
• 0
4
votes
17
replies
2.7k
views
Question about decideTests function and adj.p.value in "limma" R Package
limma
r
differential gene expression
updated 6.8 years ago by
Gordon Smyth
50k • written 6.8 years ago by
Biologist
▴ 110
0
votes
17
replies
2.4k
views
Testing for no change in RNA-seq data?
limma
limma
updated 11.2 years ago by
Simon Anders
★ 3.7k • written 11.2 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
17
replies
7.9k
views
DESeq2 Error NA values
deseq2
updated 8.9 years ago by
Michael Love
42k • written 9.0 years ago by
bharata1803
▴ 60
8
votes
17
replies
15k
views
WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
WGCNA
Sample Size
Outliers
updated 8.7 years ago by
mh.manoj
• 0 • written 9.2 years ago by
brohawndg
▴ 150
0
votes
17
replies
2.3k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 15 months ago by
Gordon Smyth
50k • written 19 months ago by
Sam
• 0
3
votes
17
replies
4.4k
views
filtering probes in affymetrix data
Annotation
limma
Annotation
limma
updated 10.3 years ago by
James W. MacDonald
65k • written 10.3 years ago by
Sabet, Julia A
▴ 180
0
votes
17
replies
2.4k
views
IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?
Microarray
illuminaHumanv2
Microarray
illuminaHumanv2
updated 10.9 years ago by
Tim Triche
★ 4.2k • written 10.9 years ago by
Simone
▴ 190
4
votes
17
replies
5.5k
views
Upgrade to 3.1 error
software error
updated 8.9 years ago by
Bogdan
▴ 670 • written 9.0 years ago by
Luobin
▴ 10
0
votes
17
replies
2.8k
views
Issue with easyRNASeq
easyRNASeq
error
8.9 years ago
ea11g0
• 0
2
votes
17
replies
1.8k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 12 months ago by
Michael Love
42k • written 12 months ago by
Alina
• 0
0
votes
17
replies
1.7k
views
How to check linear model
modalmatrix
limma
R
linear
15 months ago • updated 14 months ago
Jitendra
▴ 10
3
votes
17
replies
14k
views
DESeq2 installation error
installation
updated 6.6 years ago by
Cheng-Yuan Kao
▴ 100 • written 8.8 years ago by
seeker
• 0
0
votes
17
replies
8.3k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
Annotation
Normalization
GO
PROcess
oligo
Annotation
Normalization
GO
PROcess
oligo
updated 11.2 years ago by
James W. MacDonald
65k • written 11.2 years ago by
Kamila Naxerova
▴ 100
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 3.5 years ago by
Lluís Revilla Sancho
▴ 730 • written 7.7 years ago by
jol.espinoz
▴ 40
0
votes
17
replies
2.6k
views
Defining Weights in marrayNorm.
Microarray
Microarray
updated 20.8 years ago by
Yuk Fai Leung
▴ 100 • written 20.8 years ago by
Josef Walker
▴ 20
1
vote
17
replies
5.6k
views
Filtering out tags with low counts in DESeq and EgdeR?
Normalization
edgeR
DESeq
Normalization
edgeR
DESeq
13.0 years ago
Xiaohui Wu
▴ 280
2
votes
17
replies
3.0k
views
DESeq2- what to do when two conditions share controls?
deseq2
7.0 years ago
grashow
▴ 10
0
votes
17
replies
2.2k
views
Coverage by base
Coverage
Coverage
12.6 years ago
rohan bareja
▴ 200
1
vote
17
replies
1.8k
views
design for edgeR
edger
design matrix
glmlrt
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
simarsidhu25
• 0
4
votes
17
replies
3.2k
views
How to construct a valid GRanges object from RCPP and pass back to R
GRanges
IRanges
RCPP
Constructor
updated 6.6 years ago by
fedor.bezrukov
▴ 10 • written 6.7 years ago by
hauken_heyken
▴ 80
2
votes
17
replies
2.2k
views
How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?
MultipleComparison
edgeR
DESeq2
written 2.1 years ago by
yuet
• 0
18
votes
17
replies
4.1k
views
How to model a comparison between comparisons in edgeR?
edger
rnaseq
updated 9.2 years ago by
Ryan C. Thompson
★ 7.9k • written 9.2 years ago by
Nick N
▴ 60
22
votes
17
replies
7.3k
views
DESeq2 1.20.0 lfcshrink function
deseq2
differential expression
logfoldchange
lfcshrink
lfcthreshold
updated 3.0 years ago by
Michael Love
42k • written 5.9 years ago by
emi.sch
▴ 30
2
votes
17
replies
2.4k
views
Computationally Singular Matrices - DESeq
deseq2
rnaseq
sva
updated 18 months ago by
Michael Love
42k • written 5.1 years ago by
flippy23
• 0
0
votes
17
replies
2.3k
views
DESeq2 shrunken log fold changes
deseq2
4.1 years ago
dequattro.concetta
▴ 10
2
votes
17
replies
4.1k
views
Multi-factorial design in DEseq2: defining reduced model
deseq2
multifactorial design
reduced model
7.3 years ago
laianavarromartin
▴ 20
5
votes
16
replies
2.7k
views
Read counts generated by SGSeq are always 0
sgseq
splicing
alternative splicing
updated 8.2 years ago by
Leonard Goldstein
▴ 220 • written 8.2 years ago by
vakul.mohanty
▴ 20
0
votes
16
replies
1.9k
views
missing value
cdf
affy
affyQCReport
cdf
affy
affyQCReport
updated 15.8 years ago by
Hervé Pagès
16k • written 15.8 years ago by
Yisong Zhen
▴ 200
0
votes
16
replies
3.8k
views
Motif search -- access to JASPAR, MotIV package, more TF-PWM relationships?
Arabidopsis thaliana
MotIV
Arabidopsis thaliana
MotIV
updated 12.1 years ago by
nooshin
▴ 300 • written 12.1 years ago by
Paul Shannon
▴ 750
8
votes
16
replies
5.6k
views
Gene set enrichment analysis
gostat
gsea
gseabase
topgo
updated 9.5 years ago by
Levi Waldron
★ 1.1k • written 9.5 years ago by
kaushal Raj Chaudhary
▴ 10
0
votes
16
replies
2.3k
views
arrayQualityMetrics error
arrayQualityMetrics
arrayQualityMetrics
updated 13.3 years ago by
Manca Marco PATH
▴ 340 • written 13.3 years ago by
Paulo Nuin
▴ 200
0
votes
16
replies
2.5k
views
Variance between runs of Rsubread
rsubread
alignment
reproducibility
7.6 years ago
Isaac Virshup
• 0
3
votes
16
replies
4.4k
views
DiffBind differential binding normalization with different levels of binding
diffbind
updated 8.7 years ago by
Rory Stark
★ 5.2k • written 8.7 years ago by
igor
▴ 50
11
votes
16
replies
1.8k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma
multifactorial design
diagnostic plots
affymetrix microarrays
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
svlachavas
▴ 830
2
votes
16
replies
3.6k
views
Approaches to group the RNA-Seq samples with large heterogeneity
clustering
pca
deseq2
edger
logfoldchange
updated 8.2 years ago by
Michael Love
42k • written 8.2 years ago by
g.atla
▴ 10
8
votes
16
replies
2.7k
views
Setting package name in makeTxDbPackage
genomicfeatures
txdb
updated 9.0 years ago by
Marc Carlson
★ 7.2k • written 9.0 years ago by
Diego Diez
▴ 760
14
votes
16
replies
2.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma
toptable
8.0 years ago • updated 7.9 years ago
giroudpaul
▴ 40
8
votes
16
replies
6.3k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 3.8 years ago by
shepherl
3.9k • written 3.8 years ago by
enricoferrero
▴ 660
0
votes
16
replies
3.2k
views
Rgraphviz installation fails
rgraphviz
6.8 years ago
Giovanni Calice
▴ 160
1
vote
16
replies
2.1k
views
error installing KEGGSOAP
KEGGSOAP
KEGGSOAP
updated 11.3 years ago by
Martin Morgan
25k • written 11.3 years ago by
array chip
▴ 420
9
votes
16
replies
2.8k
views
Rsubread install fails, "unable to load shared object Rsubread.so"
rsubread
6.0 years ago
jet456
▴ 10
1
vote
16
replies
3.4k
views
error in ChAMP loading file
ChAMP
updated 9 weeks ago by
hortense96
• 0 • written 18 months ago by
Giulia
• 0
3
votes
16
replies
2.2k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 3 months ago by
shepherl
3.9k • written 2.9 years ago by
S
▴ 10
1
vote
16
replies
3.7k
views
Error: could not find function "dba"
software error
diffbind
dba
7.5 years ago
mmarins
• 0
0
votes
16
replies
2.4k
views
How does newSCESet calculate expression matrix
scater
updated 7.0 years ago by
davis
▴ 90 • written 7.0 years ago by
siajunren
• 0
3
votes
16
replies
4.2k
views
Any way to proceed duplicate removal for list of GRanges object ?
r
grangeslist
duplicate
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
Jurat Shahidin
▴ 80
4
votes
16
replies
4.7k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2
limma
combat
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
joseale2310
▴ 10
0
votes
16
replies
1.7k
views
filtering
updated 16.9 years ago by
Jenny Drnevich
★ 2.2k • written 16.9 years ago by
Lev Soinov
▴ 470
5
votes
16
replies
2.3k
views
GSVA package scores are opposite on mac and windows
GSVA
bug
gsva
bugs
updated 6.6 years ago by
Robert Castelo
★ 3.3k • written 6.6 years ago by
JasonL_Weirather
▴ 10
45,666 results • Page
5 of 914
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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