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2
replies
81
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
1 day ago • updated 4 hours ago
Yveto
• 0
0
votes
1
reply
44
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 6 hours ago by
Rory Stark
★ 5.2k • written 20 hours ago by
Ian D.
▴ 70
0
votes
0
replies
19
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
7 hours ago • updated 6 hours ago
james.zhang20
• 0
0
votes
0
replies
14
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
7 hours ago
kcarey
• 0
0
votes
3
replies
172
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 8 hours ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
0
votes
0
replies
41
views
Empty table plot using plotGseaTable()
fgsea
11 hours ago • updated 9 hours ago
Chris
• 0
0
votes
1
reply
80
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 9 hours ago by
ATpoint
★ 4.1k • written 9 hours ago by
angelathuynh5
• 0
1
vote
0
replies
22
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
9 hours ago
shepherl
3.8k
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
11 days ago • updated 10 hours ago
Chris
• 0
0
votes
3
replies
92
views
Store output of matchPWM()
biostrings
Biostrings
updated 11 hours ago by
James W. MacDonald
65k • written 14 hours ago by
mat149
▴ 70
1
vote
4
replies
438
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 11 hours ago
JKim
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
3
votes
4
replies
156
views
Help with error using camera() in limma
CAMERA
limma
1 day ago
Chris
• 0
2
votes
2
replies
1.0k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 1 day ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 1 day ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
1
reply
196
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
0
votes
3
replies
194
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 1 day ago
Chris
• 0
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
152
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 13 days ago by
Alessia
• 0
1
vote
1
reply
72
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
marcusn
• 0
0
votes
1
reply
64
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Aurora
• 0
0
votes
1
reply
77
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Agung
• 0
0
votes
0
replies
39
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
1 day ago
Maria Doyle
▴ 70
0
votes
1
reply
50
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 1 day ago by
shepherl
3.8k • written 2 days ago by
bounlu
• 0
0
votes
1
reply
70
views
putting my own expression data in deseq2
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
Dev
• 0
2
votes
2
replies
150
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
2 days ago
Chris
• 0
0
votes
0
replies
47
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
2 days ago
Chris
• 0
0
votes
4
replies
234
views
Minfi - estimatecellscount
min
minfi
updated 2 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
3
votes
3
replies
188
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 2 days ago by
ATpoint
★ 4.1k • written 3 days ago by
bioinf
▴ 10
0
votes
0
replies
65
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
7 days ago • updated 2 days ago
Sara
• 0
1
vote
1
reply
104
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 5 days ago by
Leo Lahti
▴ 40 • written 5 days ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
279
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
6 days ago • updated 5 days ago
pl23
• 0
0
votes
2
replies
176
views
PCA plot suggestions
DESeq2
PCAtools
updated 5 days ago by
Michael Love
41k • written 7 days ago by
Aaliya
• 0
1
vote
2
replies
689
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
14 days ago • updated 5 days ago
ussarizona
▴ 10
1
vote
3
replies
182
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 5 days ago by
Michael Love
41k • written 6 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
108
views
ATACseq merge peaks
DiffBind
updated 5 days ago by
ATpoint
★ 4.1k • written 7 days ago by
Shloka
• 0
1
vote
1
reply
145
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 5 days ago by
Gordon Smyth
50k • written 9 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
4
replies
294
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
7 days ago • updated 5 days ago
winwater0928
• 0
2
votes
9
replies
337
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
Alexandre
• 0
2
votes
5
replies
211
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 6 days ago by
James W. MacDonald
65k • written 8 days ago by
bandconductor
• 0
0
votes
0
replies
73
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
6 days ago
glaciya2018
• 0
1
vote
2
replies
136
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
7 days ago • updated 6 days ago
ATpoint
★ 4.1k
0
votes
2
replies
229
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
9 days ago • updated 6 days ago
shuwangxinze1996
• 0
0
votes
8
replies
318
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 days ago by
swbarnes2
★ 1.3k • written 8 days ago by
Aaliya
• 0
0
votes
1
reply
124
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
kcarey
• 0
1
vote
13
replies
367
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
10 days ago • updated 7 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
234
views
get BM error
ensembldb
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
Fara
• 0
0
votes
5
replies
284
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 7 days ago by
James W. MacDonald
65k • written 10 days ago by
Gayatri
• 0
0
votes
0
replies
68
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
7 days ago
Dario Strbenac
★ 1.5k
45,602 results • Page
1 of 913
Recent ...
Replies
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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