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0
votes
0
replies
33
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
1 day ago
Chris
• 0
0
votes
0
replies
63
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
5 days ago
glaciya2018
• 0
0
votes
0
replies
58
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
6 days ago • updated 1 day ago
Sara
• 0
0
votes
0
replies
61
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
6 days ago
Dario Strbenac
★ 1.5k
0
votes
8
replies
308
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 5 days ago by
swbarnes2
★ 1.3k • written 7 days ago by
Aaliya
• 0
0
votes
2
replies
206
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
7 days ago • updated 5 days ago
shuwangxinze1996
• 0
1
vote
13
replies
351
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
9 days ago • updated 5 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
68
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
9 days ago
vaxahey107
• 0
0
votes
0
replies
85
views
I am trying to detect alternative splicing.
ASpli
10 days ago
Sebashish
• 0
0
votes
0
replies
105
views
Warning while loading DEP package
DEP
updated 12 days ago by
shepherl
3.8k • written 12 days ago by
Namrata
• 0
1
vote
2
replies
197
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
12 days ago • updated 11 days ago
Le
• 0
1
vote
2
replies
139
views
Error in champ.load(): The following specified files do not exist
ChAMP
12 days ago
Sherin
• 0
0
votes
1
reply
88
views
Input Question for deseq.r
RSeqAn
updated 12 days ago by
ATpoint
★ 4.1k • written 13 days ago by
Nina
• 0
0
votes
4
replies
210
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
13 days ago • updated 10 days ago
lonn
• 0
0
votes
0
replies
70
views
Enzyme Engineering
BioTIP
13 days ago
bocchemistry
• 0
0
votes
0
replies
84
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
14 days ago • updated 13 days ago
Maliha Tabassum
• 0
0
votes
1
reply
109
views
what is the sampleFiles
chipseq
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
zhulin
• 0
0
votes
0
replies
84
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
14 days ago
Virangika
• 0
0
votes
0
replies
62
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
15 days ago
Henry
▴ 10
0
votes
1
reply
119
views
Deseq2 Rlog transformation
DESeq2
updated 15 days ago by
ATpoint
★ 4.1k • written 16 days ago by
Sahar
• 0
2
votes
2
replies
159
views
[DiffBind] Obtaining normalization factors
DiffBind
18 days ago • updated 14 days ago
Henry
▴ 10
0
votes
3
replies
238
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 12 days ago by
W. Evan Johnson
▴ 850 • written 18 days ago by
schlumbohm
• 0
0
votes
0
replies
82
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
18 days ago
Stevie Pederson
• 0
3
votes
6
replies
257
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
19 days ago
nhaus
▴ 30
0
votes
1
reply
164
views
DESeq2 gives an error and R crashes
DESeq2
19 days ago • updated 18 days ago
Shefali
• 0
0
votes
0
replies
120
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
19 days ago
Eryn
• 0
0
votes
0
replies
80
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
20 days ago
Dennis
• 0
0
votes
1
reply
144
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 16 days ago by
Guido Hooiveld
★ 3.9k • written 20 days ago by
Lucie
• 0
0
votes
0
replies
100
views
ggtree tip label position (depth)
ggtree
21 days ago • updated 20 days ago
Roope
• 0
2
votes
6
replies
371
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
22 days ago • updated 21 days ago
Chris
• 0
0
votes
0
replies
136
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
25 days ago
andromeda
• 0
0
votes
1
reply
120
views
Granges regionCounts not returning the expected number of entries
methylKit
25 days ago • updated 24 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
92
views
flowDensity on a flowset
flowDensity
25 days ago
fredrikwallberg
• 0
0
votes
0
replies
82
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
26 days ago
Macsue
• 0
0
votes
1
reply
148
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 28 days ago by
James W. MacDonald
65k • written 29 days ago by
ja569116
• 0
0
votes
2
replies
282
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
29 days ago • updated 25 days ago
fer_talavera
• 0
0
votes
2
replies
244
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 11 days ago
isaac.vock
• 0
0
votes
7
replies
364
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
4 weeks ago • updated 28 days ago
needNGS
• 0
0
votes
0
replies
104
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
4 weeks ago
feather-W
• 0
0
votes
0
replies
103
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
4 weeks ago
Ankit
▴ 20
1
vote
5
replies
326
views
fgsea fork
fgsea
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
yimjohns
• 0
0
votes
0
replies
89
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
4 weeks ago
Pierre Lindenbaum
▴ 10
3
votes
3
replies
379
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 5 weeks ago by
alan.ocallaghan
▴ 160 • written 5 weeks ago by
Najla Abassi
• 0
0
votes
0
replies
111
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
5 weeks ago
gshweta95
• 0
2
votes
1
reply
200
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 5 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 weeks ago by
enee
▴ 10
0
votes
0
replies
111
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
5 weeks ago
nromerov
• 0
1
vote
3
replies
254
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 5 weeks ago by
Marcel Ramos
690 • written 5 weeks ago by
Astrid Deschênes
• 0
0
votes
0
replies
122
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
5 weeks ago
mayra.haedo
• 0
0
votes
0
replies
109
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
5 weeks ago
taylor.witte
• 0
0
votes
0
replies
130
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
5 weeks ago
erbrocato
• 0
1,000 results • Page
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Replies
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma
by
James W. MacDonald
65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! That is a great tip. cameraRes <- camera(numeric_matrix, geneSets, inter.gene.cor=0.01, design) Error in Stat[iset]…
Votes
Answer: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
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to
James W. MacDonald
65k
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to
jeffrey.maurer
• 0
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Chris
• 0
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Leonard Goldstein
▴ 200
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▴ 1000
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