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0
votes
0
replies
6
views
Produce quantile normalized expression values for use with BatchQC
BatchQC
1 hour ago
Josh
• 0
0
votes
1
reply
35
views
How to plot the RMA log2 normalised data from Affymetrix
log2
RMA
Affymetrix
affy
Normalization
1 day ago
Lara
• 0
• updated 11 hours ago
Kevin Blighe
2.5k
0
votes
0
replies
23
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
11 hours ago
robert.chen
• 0
0
votes
0
replies
18
views
ribosomeProfilingQC - countReads function - is it possible to consider library type - non-stranded, forward-stranded or rev-stransded?
ribosomeProfilingQC
countReads
13 hours ago
alexandr.gopanenko
• 20
0
votes
2
replies
41
views
Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
1 day ago
yueli7
• 10
• updated 11 hours ago
Kevin Blighe
2.5k
0
votes
0
replies
32
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
1 day ago
Marina
• 0
0
votes
2
replies
36
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R
oligoClasses
Oligoclass
Bioconductor
Oligo
1 day ago
tanya
• 0
• updated 1 day ago
Martin Morgan
25k
0
votes
3
replies
100
views
Unable to upload an App in shinyapps.io with bioconductor packages
shinny
graph
RBGL
10 days ago
Xavier-Andoni
• 0
• updated 2 days ago
Marcel Ramos
490
1
vote
2
replies
66
views
Question about nearest function in R package IRanges
nearest
IRanges
2 days ago
junhui.li11
• 0
• updated 1 day ago
Julie Zhu
♦ 4.3k
1
vote
1
reply
44
views
How to install Ghostscript in windows?
RnBeads.hg19
RnBeads
2 days ago
Federica
• 0
• updated 2 days ago
mscherer
• 50
0
votes
5
replies
1.0k
views
assayData: 0 features
geoquery
5.5 years ago
Ed Siefker
• 230
• updated 2 days ago
H. Zadeh
• 0
0
votes
2
replies
46
views
Pair-wise DESeq2 using tximport (running time and multi-threading)
tximport
DESeq2
2 days ago
Marcus
• 0
• updated 2 days ago
Michael Love
32k
0
votes
1
reply
38
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
5 days ago
Bethan
• 0
• updated 2 days ago
bastien.ducreux
• 0
3
votes
6
replies
170
views
Is it possible to create `HDF5Array` Delayed Arrays from HDF5 files hosted on S3?
TileDBArray
HDF5Array
MultiAssayExperiment
7 days ago • updated 1 day ago
Thomas Sandmann
• 80
1
vote
2
replies
47
views
error in DESeq2 results(dds)
DESeq2
datasetfrommatrix
results
error
2 days ago
james
• 0
0
votes
0
replies
27
views
dmrseq on a subset of genomic regions
dmrseq
3 days ago
KIR_F
• 0
0
votes
1
reply
52
views
plotSex error message
minfiData
plotsex
minfi
minfiDataEPIC
r
3 days ago
Bethan
• 0
• updated 2 days ago
suman
• 0
0
votes
0
replies
21
views
iupac2meme function missing in universalmotif package
universalmotif
3 days ago
lessismore
• 0
0
votes
0
replies
22
views
combineTwoExpressionSet from a4Base is not working properly
a4Base
3 days ago
irene.roman
• 0
0
votes
0
replies
39
views
MEDIPS - export wig with normalized counts
MEDIPS
4 days ago
lshepard
• 40
2
votes
2
replies
54
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF
GenomicFeatures
4 days ago • updated 3 days ago
erhoppe
• 0
0
votes
3
replies
58
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq
DiffBind
4 days ago • updated 3 days ago
Asma
• 0
2
votes
4
replies
72
views
How to launch the RnBeads Data Juggler?
RnBeads
4 days ago
Federica
• 0
1
vote
4
replies
66
views
goseq package loading issues
DESeq2
goseq
4 days ago • updated 3 days ago
avinashi
• 0
1
vote
1
reply
44
views
How to find the source code of the package STRINGdb ?
STRINGdb
Bioconductor
4 days ago
deepue
• 10
• updated 4 days ago
shepherl
2.5k
1
vote
2
replies
79
views
Regarding transcripts to gene ID conversion in tximport
salmon
tximport
DESeq2
4 days ago • updated 3 days ago
Nikolay Ivanov
• 0
0
votes
0
replies
36
views
error during installation of 'DEseq2' package
DESeq2
Install
4 days ago
su
• 0
• updated 4 days ago
Kevin Blighe
2.5k
3
votes
2
replies
74
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData
DEGreport
edgeR
5 days ago • updated 4 days ago
Wuschel
• 10
2
votes
2
replies
65
views
How to download KEGG pathways for list of enriched genes
RNASeqRData
GO
4 days ago
Wuschel
• 10
2
votes
3
replies
74
views
DESeq2 extracting relevant contrasts with interactions
DESeq2
DifferentialExpression
5 days ago
jd348
• 0
• updated 4 days ago
Michael Love
32k
0
votes
1
reply
62
views
Using tximport to create the input for DESeq2
RNASeqR
5 days ago
ahmesalama
• 0
• updated 4 days ago
Michael Love
32k
0
votes
0
replies
38
views
ENmix: how to combine oxBS.MLE with RCP?
ENmix
5 days ago
joannew
• 0
0
votes
2
replies
68
views
How to setup sample design in DESeq2
DESeq2
5 days ago
dequattro.concetta
• 10
• updated 5 days ago
swbarnes2
• 630
5
votes
5
replies
116
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
5 days ago
H. Zadeh
• 0
• updated 5 days ago
James W. MacDonald
56k
0
votes
10
replies
120
views
Exporting DESeq2 filtered results
DESeq2
5 days ago • updated 4 days ago
Laura
• 0
2
votes
3
replies
74
views
ANOVA Limma
ANOVA
limma
5 days ago
georgina.fqw
• 10
• updated 5 days ago
James W. MacDonald
56k
2
votes
2
replies
65
views
mmusculus GO terms with Biomart
biomaRt
GOTerms
6 days ago • updated 5 days ago
salvin
• 0
0
votes
0
replies
32
views
WGCNA: Module preservation vs consensus analysis
WGCNA
wgcna
5 days ago
Colari19
• 10
1
vote
2
replies
65
views
How to define settings for design primers with openPrimeR?
openPrimeR
6 days ago • updated 19 hours ago
marongiu.luigi
• 0
0
votes
3
replies
732
views
An ESR essay about software design, and how it applies to Bioconductor
GUI
GUI
17.0 years ago
Ann Loraine
• 30
0
votes
2
replies
92
views
TPM data in limma/voom
voom
limma
DifferentialExpression
edgeR
6 days ago • updated 5 days ago
RJM
• 0
0
votes
0
replies
27
views
mpralm error
mpra
6 days ago
gywang912
• 0
1
vote
4
replies
79
views
Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker
TxDb.Mmusculus.UCSC.mm10.knownGene
6 days ago • updated 5 days ago
Kasit
• 0
0
votes
0
replies
28
views
enrichPathway error when checking condition lengths used
DOSE
ReactomePA
6 days ago
Lluís Revilla Sancho
• 610
0
votes
0
replies
22
views
Exclude background correction in NADfinder
NADfinder
6 days ago
eva.pinatel
• 10
0
votes
3
replies
77
views
deseq2 design with two variables
DESeq2
6 days ago
sj
• 0
• updated 6 days ago
Michael Love
32k
3
votes
4
replies
124
views
Identifying differentially expressed genes
identifyingDifferentiallyexpressedgenes
DESeq2
7 days ago
MOHAMMAD
• 0
• updated 6 days ago
ATpoint
• 450
2
votes
4
replies
117
views
biomaRt - getBM; Error with obtaining a dataset from getBM() function
biomaRt
error
getBM
7 days ago
Zen
• 10
• updated 6 days ago
Mike Smith
♦ 4.8k
2
votes
8
replies
219
views
Dealing with my.contrasts with replicates containing nested samples
edgeR
9 days ago • updated 3 days ago
James
• 0
0
votes
2
replies
92
views
WGCNA - Outliers after creating sample tree
MicroarrayData
WGCNA
Microarray
9 days ago • updated 6 days ago
jpwl2
• 0
65 results • Page
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Comment: Error: Aesthetics must be either length 1 or the same as the data (1): x and xen
by
Kevin Blighe
2.5k
Thank you for posting the answer.
Answer: How to plot the RMA log2 normalised data from Affymetrix
by
Kevin Blighe
2.5k
Hi Lara, It may be a good idea to go through one of the workflows in their entirety. This would help you to better understand the data p…
Comment: How to define settings for design primers with openPrimeR?
by
marongiu.luigi
• 0
I see. I tried to upload settings but: ``` > library("openPrimeR") There are missing/non-functioning external tools. To use the full potent…
Comment: Error: Aesthetics must be either length 1 or the same as the data (1): x and xen
by
yueli7
• 10
I knew what I am wrong . plotEnrichment(pathways.kegg[["KEGG_PYRIMIDINE_METABOLISM"]], ranks) It should be "ranks", not exampleRan…
Comment: Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
by
Martin Morgan
25k
This type of error usually means that you are mixing Bioconductor packages from different releases. Try ``` BiocManager::version() # Shoul…
Votes
Answer: How to define settings for design primers with openPrimeR?
Answer: Question about nearest function in R package IRanges
Answer: How to install Ghostscript in windows?
Answer: error in DESeq2 results(dds)
Answer: Is it possible to create `HDF5Array` Delayed Arrays from HDF5 files hosted on S3
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