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6
votes
7
replies
3.8k
views
GOexpress: use DESeq2 data object as input
GOexpress
deseq2
expressionset
8.6 years ago
martin.hoelzer
▴ 20
0
votes
8
replies
1.6k
views
GOstats error messages
Annotation
rat2302
Annotation
rat2302
18.6 years ago
Kimpel, Mark W
▴ 890
0
votes
6
replies
2.2k
views
error installing Rgraphviz
Rgraphviz
PROcess
BiocInstaller
Rgraphviz
PROcess
BiocInstaller
updated 11.9 years ago by
Dan Tenenbaum
★ 8.2k • written 11.9 years ago by
Mark Miller
▴ 10
0
votes
6
replies
3.6k
views
batch effect confounded with condition
GO
limma
GO
limma
12.2 years ago • updated 12.1 years ago
Tefina Paloma
▴ 220
1
vote
10
replies
3.0k
views
ShortRead with large fastq files
shortread
8.9 years ago
danova_fr
▴ 20
0
votes
11
replies
1.5k
views
Rgraphviz: adding weight to an edge
updated 18.4 years ago by
Jeff Gentry
★ 3.9k • written 18.4 years ago by
Kaustubh Patil
▴ 110
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 • updated 12.9 years ago
Xiaohui Wu
▴ 280
0
votes
9
replies
19k
views
dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : replacement has 0 rows, data has 1963
dmrcate
updated 7.3 years ago by
Tim Peters
▴ 170 • written 7.5 years ago by
ew17
• 0
0
votes
21
replies
6.6k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 5 months ago by
Marge
• 0 • written 11.3 years ago by
José Luis Lavín
▴ 280
0
votes
6
replies
1.4k
views
memory requirement
updated 21.4 years ago by
Liaw, Andy
▴ 360 • written 21.4 years ago by
Yi-Xiong Zhou
▴ 10
2
votes
10
replies
2.6k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
9.2 years ago
n.kreim
▴ 20
0
votes
5
replies
1.2k
views
pa.calls-function in package "panp"
updated 13.7 years ago by
Fong Chun Chan
▴ 130 • written 13.7 years ago by
Samuel Wuest
▴ 330
0
votes
5
replies
2.0k
views
MassiR Gender Prediction on Affy microarrays
microarray
affy
massiR
8.6 years ago
t.demooij
• 0
6
votes
7
replies
2.9k
views
Error: Failed to set session genome to...
gviz
rtracklayer
updated 8.6 years ago by
florian.hahne@novartis.com
★ 1.6k • written 9.0 years ago by
liz.ingsimmons
▴ 140
0
votes
5
replies
1.7k
views
Annotation package built with pdInfoBuilder cannot be installed
annotation
pdinfobuilder
9.1 years ago
alakatos
▴ 130
0
votes
11
replies
2.6k
views
package 'ChAMP' demo/test code fails at champ.CNA()
software error
updated 7.3 years ago by
Yuan Tian
▴ 90 • written 9.3 years ago by
Hamid Bolouri
▴ 90
2
votes
5
replies
3.2k
views
Problem encountered when running GSVA for RNAseq
gsva
rnaseq
updated 9.5 years ago by
Robert Castelo
★ 3.3k • written 9.5 years ago by
polly0806
• 0
1
vote
8
replies
2.0k
views
methylPipe meth.call issue with sorted SAM file
methylpipe
updated 3.1 years ago by
Macarena
• 0 • written 7.9 years ago by
slbattle
▴ 10
2
votes
7
replies
1.4k
views
Factoring analysis and better design
deseq2
deseq
7.7 years ago
arabella23
• 0
0
votes
9
replies
1.6k
views
is-normalisation-really-required
limma
limma
19.1 years ago
vijayaraj nagarajan
▴ 80
0
votes
5
replies
2.8k
views
retrieve human readable gene names from KEGG identifiers
kegggraph
8.2 years ago
Osvaldo
▴ 40
0
votes
11
replies
2.1k
views
Rsubread/Rsamtools mappings outside of chromosome ranges
PROcess
Rsamtools
Rsubread
TCC
PROcess
Rsamtools
Rsubread
TCC
12.2 years ago
Thomas Girke
★ 1.7k
6
votes
11
replies
2.6k
views
edgeR on microRNA data
microRNA
edgeR
miRNA
12.6 years ago • updated 2.9 years ago
Gordon Smyth
50k
0
votes
12
replies
998
views
limma help - choosing an approach
updated 17.6 years ago by
Gordon Smyth
50k • written 17.6 years ago by
john seers IFR
▴ 810
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
0
votes
6
replies
1.4k
views
Rat Nimblegen promoter dataset HOWTO
Rattus norvegicus
Rattus norvegicus
updated 16.3 years ago by
Straubhaar, Juerg
▴ 300 • written 16.3 years ago by
Dario Greco
▴ 310
0
votes
6
replies
957
views
BSgenome package - add the bos taurus genome
updated 16.1 years ago by
Hervé Pagès
16k • written 16.2 years ago by
João Fadista
▴ 500
0
votes
5
replies
3.6k
views
How to import data to R
annotation
updated 8.2 years ago by
arfranco
▴ 130 • written 8.2 years ago by
xlyan011
• 0
0
votes
9
replies
1.4k
views
matrix row/column displayed as a list
Cancer
Cancer
updated 17.1 years ago by
Seth Falcon
★ 7.4k • written 17.1 years ago by
Daniel Brewer
★ 1.9k
0
votes
6
replies
1.5k
views
multiple testing with 54000 genes
19.2 years ago
Dipl.-Ing. Johannes Rainer
▴ 430
0
votes
7
replies
3.0k
views
Is anyone able to explain the statistics behind the dmpFinder function in minfi package?
minfi
methylation
dmpfinder
limma
updated 7.0 years ago by
vulegom
• 0 • written 7.6 years ago by
mcall
▴ 20
0
votes
11
replies
1.8k
views
Upgrading R
PROcess
PROcess
updated 15.0 years ago by
Michal Blazejczyk
▴ 320 • written 15.0 years ago by
Sarmah, Chintanu Kumar
▴ 70
0
votes
9
replies
2.5k
views
How to do k-fold validation using SVM
updated 21.3 years ago by
Stephen Henderson
★ 1.0k • written 21.3 years ago by
Song, Guangchun
▴ 30
0
votes
9
replies
1.4k
views
RMA normalization when using subsets of samples
updated 18.2 years ago by
Ron Ophir
▴ 270 • written 18.2 years ago by
Sylvia.Merk@ukmuenster.de
▴ 60
0
votes
9
replies
1.2k
views
limma question
updated 18.2 years ago by
Sun, Yezhou
▴ 30 • written 18.2 years ago by
Michael Stapelberg
▴ 30
0
votes
6
replies
1.2k
views
ABPkgBuilder (AnnBuilder) subscript out of bounds error
18.2 years ago
Henrik Hornshøj Jensen
▴ 90
0
votes
17
replies
2.4k
views
regarding web interface to R coding
updated 14.7 years ago by
Steve Lianoglou
★ 13k • written 14.7 years ago by
ankhee dutta
▴ 60
1
vote
5
replies
3.5k
views
Finding Out the Fold Changes
updated 20.5 years ago by
James W. MacDonald
65k • written 20.5 years ago by
Sachin Mathur
▴ 60
0
votes
6
replies
1.4k
views
replicates and low expression levels
affy
affy
updated 20.9 years ago by
Stephen Henderson
★ 1.0k • written 20.9 years ago by
rgentleman
★ 5.5k
0
votes
7
replies
1.8k
views
recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9
GUI
GUI
20.1 years ago • updated 20.0 years ago
Marc Salit
▴ 80
0
votes
6
replies
1.3k
views
Cel file error
updated 20.4 years ago by
A.J. Rossini
▴ 810 • written 20.4 years ago by
Jason Hipp
▴ 40
2
votes
6
replies
2.5k
views
ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker
covplot
ENCODE
ChIpseq
9.0 years ago
sarabusquets88
• 0
1
vote
6
replies
2.2k
views
Detect short tandem repetitions from bam file
bam
short tandem repetitions
package
8.5 years ago
Pau Marc Muñoz Torres
▴ 20
3
votes
5
replies
2.5k
views
Work with GRanges objects in DiffBind
diffbind
updated 7.8 years ago by
termanini
▴ 10 • written 8.7 years ago by
xulong.wang
• 0
0
votes
12
replies
3.4k
views
problems when trying to use biomaRt
GUI
biomaRt
GUI
biomaRt
updated 14.1 years ago by
Jenny Drnevich
★ 2.0k • written 14.1 years ago by
Juan Pablo Fededa
▴ 50
0
votes
9
replies
1.5k
views
writing of /usr/lib/R
updated 18.5 years ago by
Shi, Tao
▴ 720 • written 18.5 years ago by
Michael Green
▴ 20
3
votes
5
replies
1.4k
views
Error in biomaRt User Guide example Task 11
biomaRt
updated 7.6 years ago by
Thomas Maurel
▴ 800 • written 7.6 years ago by
cring
▴ 10
8
votes
11
replies
9.4k
views
Filtering of RNA-seq data in EdgeR
rnaseq
edger
filtering
updated 7.8 years ago by
David ROUX
▴ 20 • written 7.9 years ago by
alireza_sharifian_10
▴ 10
3
votes
8
replies
10k
views
RDAVIDWebService - Unable to sendViaPost to url etc etc - server time out
software error
david
rdavidwebservice
updated 8.7 years ago by
oops324
• 0 • written 9.1 years ago by
TriS
▴ 200
0
votes
9
replies
2.5k
views
MEDIPS: how does MEDIPS define a methylated region / cluster?
Sequencing
MEDIPS
updated 9.6 years ago by
mengru1223
• 0 • written 9.7 years ago by
Guest User
★ 13k
45,611 results • Page
4 of 913
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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