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0
votes
0
replies
827
views
Is it normal that normalize.loess does not tolerate a single NA value?
15.2 years ago
Emmanuel Levy
▴ 270
0
votes
0
replies
560
views
Creating a substet of probe intensities from AffyBatch object
probe
affy
probe
affy
19.7 years ago
Larry La Pointe
▴ 60
0
votes
0
replies
1.2k
views
Rsamtools insert size
rsamtools
samtools
bam
bowtie2
6.3 years ago
igor
▴ 50
0
votes
3
replies
1.5k
views
Problem getting soft threshold power using WGCNA for RNA-seq data
RNASeq
WGCNA
2.5 years ago
jms2520
▴ 10
0
votes
0
replies
686
views
MarrayNorm question.
20.4 years ago
Jean Yee Hwa Yang
▴ 920
0
votes
0
replies
1.8k
views
Monocle-strange differential expression results
monocle
differential expression
8.4 years ago
sunil.mangalam
• 0
0
votes
0
replies
1.0k
views
EBSeq Results Affected By Outlying Values
EBSeq
EBSeq
10.3 years ago
Dario Strbenac
★ 1.5k
0
votes
2
replies
1.2k
views
calculating TSS enrichment from ATACseq data
GenomicRanges
Views
ATACseq
TSS
5.0 years ago
tangming2005
▴ 190
0
votes
1
reply
4.4k
views
Conversion to SingleCellExperiment from Seurat objects
Seurat
SingleCellExperiment
6.0 years ago
Wolfgang Huber
★ 13k
0
votes
0
replies
400
views
Design for linear model
statistic
4.5 years ago
ijvechetti
▴ 10
0
votes
0
replies
769
views
Comparing normal versus tumor specimens from different studies
Microarray
Cancer
Breast
Microarray
Cancer
Breast
17.8 years ago
raffaele calogero
▴ 500
0
votes
0
replies
847
views
normalize GFP expression by cell size and graph with densityplot
graph
graph
12.0 years ago
Chandra Jack
▴ 90
0
votes
0
replies
915
views
Limma: Array weights question
15.3 years ago
Gordon Smyth
50k
0
votes
0
replies
657
views
beadarray vignette has broken code in R2.14.1?
illuminaHumanv2
limma
GEOquery
beadarray
illuminaHumanv2
limma
GEOquery
beadarray
12.2 years ago
Henriquez, Nick
▴ 20
0
votes
0
replies
510
views
Error in snpStats::read.pedfile: GeneGeneInter
snpmatrix
ped
6.4 years ago
GENOMIC_region
• 0
0
votes
1
reply
1.2k
views
flowDensity loop on flowSet
flowdensity
flowcore
for loop
updated 5.3 years ago by
Bioconductor Community
0 • written 5.5 years ago by
beshea.jj
• 0
0
votes
0
replies
1.2k
views
CRISPRseek: create own org.Hs.eg.db package
CRISPRseek
org.hs.eg.db
8.9 years ago
Julie Zhu
★ 4.3k
0
votes
0
replies
715
views
GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip
Normalization
probe
gcrma
Normalization
probe
gcrma
15.9 years ago
Siobhan A. Braybrook
▴ 50
0
votes
0
replies
715
views
unbiased filtering of paired dataset
11.6 years ago
Guido Hooiveld
★ 4.0k
0
votes
0
replies
872
views
annotation dbi for miRNA 2.0 Array
miRNA
Annotation
miRNA
Annotation
12.6 years ago
Guest User
★ 13k
0
votes
0
replies
747
views
Problem with obtaining annotation of mgu74av2 chip
Cancer
mgu74av2
probe
annotate
annaffy
Cancer
mgu74av2
probe
annotate
annaffy
20.0 years ago
Richard Friedman
★ 2.0k
0
votes
0
replies
610
views
Quantile normailization and NA
Normalization
Normalization
18.9 years ago
Ravi Murthy
▴ 10
0
votes
0
replies
795
views
Allele-specific copy numbers using 450K Illumina methylation microarrays
10.0 years ago
Aaerp
▴ 40
0
votes
0
replies
503
views
when to use filter_by_cv() function from the lipidr package
Lipidomics
lipidr
lipi
3.5 years ago
eme
• 0
0
votes
0
replies
914
views
CGHcall problem
CGH
CGHcall
CGH
CGHcall
14.1 years ago
Erik Dassi
▴ 10
0
votes
0
replies
597
views
repository
reposTools
reposTools
20.6 years ago
Arne.Muller@aventis.com
▴ 620
0
votes
0
replies
962
views
R function to deconvolve ESI MS spectra of multiple charge large biopolymers
mass spectrometry
R
mzR
6.1 years ago
andreas.breidbach
• 0
0
votes
0
replies
679
views
Bioconductor and the Google Summer of Code
11.1 years ago
Marc Carlson
★ 7.2k
0
votes
0
replies
2.4k
views
DiffBind annotation
Annotation
ChIPpeakAnno
DiffBind
chipenrich
9.7 years ago
Rory Stark
★ 5.2k
0
votes
0
replies
902
views
Low logFCs using MAST for scRNA-seq
MAST
2.1 years ago
learner_MD
• 0
1
vote
2
replies
843
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
21 months ago
Delta._.43
▴ 20
0
votes
0
replies
437
views
interactiveDisplay build error
interactiveDisplay
2.2 years ago
starsareintherose
• 0
0
votes
1
reply
605
views
Affymetrix microarray - Limma on timepoint experiment, how to make the design and contrast matrix ?
limma
R
microarray
timepoint
affy
updated 4.1 years ago by
shepherl
3.9k • written 4.1 years ago by
ashwinmenon1994
• 0
0
votes
1
reply
470
views
How to adjust plots generated using psygenet2r?
psygenet2r
updated 13 months ago by
helucro
▴ 70 • written 14 months ago by
marinaw
▴ 20
0
votes
0
replies
672
views
xcms crashes R 4.2.0, also unable to install IPO or msdata
IPO
msdata
xcms
2.0 years ago
mba
• 0
0
votes
0
replies
923
views
request: calculate coverage with weight on RangedData object
Coverage
Cancer
IRanges
Coverage
Cancer
IRanges
14.2 years ago
Janet Young
▴ 740
0
votes
0
replies
637
views
TFutils database
TFutils
mouse
gene
convert
3.0 years ago
nicocillari
• 0
0
votes
0
replies
573
views
simLL method in GOstats
GO
graph
GO
graph
19.1 years ago
Seth Falcon
★ 7.4k
0
votes
0
replies
571
views
Made a pDATA manually for HTqPCR procedure
HTqPCR
phenoData
esetVis
pData
2.6 years ago
Marcelo Laia
▴ 450
0
votes
3
replies
946
views
Social Network Login Failure
software error
8.8 years ago
MarcinKosiński
• 0
1
vote
1
reply
612
views
Any possiblity applying
WGCNA
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
adR
▴ 30
0
votes
4
replies
1.8k
views
ChemmineOB installation failed
software error
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
abdullahsaeed92
• 0
0
votes
0
replies
1.1k
views
Interpretation of control strip and beta density plots for Illumina methylation array data using minFi
minfi
methylation
EPIC
5.8 years ago
sichan
• 0
0
votes
0
replies
893
views
Problems reading multiple MAQ map files with ShortRead ReadAligned
ShortRead
charm
ShortRead
charm
15.2 years ago
David Rossell
▴ 100
0
votes
0
replies
824
views
pvaluecutoff meaning in enrichKEGG
KEGG
RNAseq
4.6 years ago
sportiellomike
• 0
0
votes
0
replies
759
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings
alignment
5.1 years ago
Juliet Hannah
▴ 360
0
votes
0
replies
1.3k
views
ISMB talks: Pathview for pathway-based data integration and visualization
Pathways
Visualization
pathview
Pathways
Visualization
pathview
9.9 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
643
views
Best way of presenting a sub-fraction of edgeR RNAseq gene expression results in a publication
edgeR
edgeR
10.3 years ago
Gordon Smyth
50k
0
votes
0
replies
1.0k
views
Unclear error in getBM() with attributes and output
getBM
software error
9.0 years ago
kris.petrini
• 0
0
votes
0
replies
969
views
GEOQuery - Encoding UTF-8
geoquery
UTF
7.8 years ago
Adrian Johnson
▴ 330
1,000 results • Page
1 of 20
Recent ...
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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…
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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Vincent J. Carey, Jr.
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Koen Van den Berge
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shepherl
3.9k
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Ken C
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