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6
votes
19
replies
2.4k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 14 hours ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 14 hours ago
Chris
• 0
8
votes
6
replies
1.6k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 hours ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 11 hours ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
10 days ago • updated 3 hours 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 11 hours ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
1
vote
3
replies
837
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 6 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
684
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
13 days ago • updated 4 days ago
ussarizona
▴ 10
1
vote
13
replies
355
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
9 days ago • updated 6 days ago
fernanda.backsouza
▴ 10
2
votes
9
replies
328
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 5 days ago by
James W. MacDonald
65k • written 5 days ago by
Alexandre
• 0
0
votes
8
replies
310
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 6 days ago by
swbarnes2
★ 1.3k • written 7 days ago by
Aaliya
• 0
0
votes
5
replies
278
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 6 days ago by
James W. MacDonald
65k • written 9 days ago by
Gayatri
• 0
1
vote
4
replies
277
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
6 days ago • updated 4 days ago
winwater0928
• 0
1
vote
7
replies
259
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
5 days ago • updated 4 days ago
pl23
• 0
0
votes
4
replies
229
views
Minfi - estimatecellscount
min
minfi
updated 1 day ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
2
votes
5
replies
226
views
get BM error
ensembldb
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
Fara
• 0
0
votes
2
replies
215
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
8 days ago • updated 6 days ago
shuwangxinze1996
• 0
2
votes
5
replies
206
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 5 days ago by
James W. MacDonald
65k • written 7 days ago by
bandconductor
• 0
1
vote
3
replies
189
views
Different Shrunk Log2FC according with reference
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
183
views
minfi::read.metharray.exp
minfiData
minfi
updated 6 days ago by
Basti
▴ 780 • written 8 days ago by
clacarion
• 0
0
votes
3
replies
173
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 13 hours ago by
James W. MacDonald
65k • written 1 day ago by
SSSJec
• 0
3
votes
3
replies
172
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 1 day ago by
ATpoint
★ 4.1k • written 2 days ago by
bioinf
▴ 10
1
vote
3
replies
171
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 4 days ago by
Michael Love
41k • written 5 days ago by
JalapenoCornbread
• 0
0
votes
2
replies
164
views
PCA plot suggestions
DESeq2
PCAtools
updated 4 days ago by
Michael Love
41k • written 6 days ago by
Aaliya
• 0
0
votes
3
replies
144
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 14 hours ago by
Alejandro Reyes
★ 1.9k • written 12 days ago by
Alessia
• 0
1
vote
1
reply
139
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 4 days ago by
Gordon Smyth
50k • written 8 days ago by
Lluís Revilla Sancho
▴ 730
2
votes
2
replies
137
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
1 day ago
Chris
• 0
1
vote
2
replies
128
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
6 days ago • updated 5 days ago
ATpoint
★ 4.1k
0
votes
1
reply
118
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 6 days ago by
Michael Love
41k • written 6 days ago by
kcarey
• 0
3
votes
4
replies
108
views
Help with error using camera() in limma
CAMERA
limma
14 hours ago • updated 10 hours ago
Chris
• 0
0
votes
1
reply
108
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 11 hours ago by
James W. MacDonald
65k • written 1 day ago by
SSSJec
• 0
0
votes
1
reply
98
views
ATACseq merge peaks
DiffBind
updated 4 days ago by
ATpoint
★ 4.1k • written 6 days ago by
Shloka
• 0
1
vote
1
reply
96
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 4 days ago by
Leo Lahti
▴ 40 • written 4 days ago by
Dario Strbenac
★ 1.5k
0
votes
0
replies
66
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
63
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
6 days ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
60
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
6 days ago • updated 1 day ago
Sara
• 0
0
votes
1
reply
54
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 16 hours ago by
Michael Love
41k • written 1 day ago by
Agung
• 0
0
votes
1
reply
50
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 16 hours ago by
Michael Love
41k • written 17 hours ago by
marcusn
• 0
0
votes
1
reply
49
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 16 hours ago by
Michael Love
41k • written 22 hours ago by
Aurora
• 0
0
votes
1
reply
47
views
putting my own expression data in deseq2
DESeq2
updated 19 hours ago by
ATpoint
★ 4.1k • written 20 hours ago by
Dev
• 0
0
votes
1
reply
43
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 17 hours ago by
shepherl
3.8k • written 1 day ago by
bounlu
• 0
0
votes
0
replies
35
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
25
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
17 hours ago
Maria Doyle
▴ 70
0
votes
0
replies
20
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
7 hours ago
HAK
• 0
0
votes
0
replies
17
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
5 hours ago • updated 4 hours ago
Yveto
• 0
45 results • Page
1 of 1
Recent ...
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Answer: SGSeq: moving toward diffex from SGSeq analysis
by
Leonard Goldstein
▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
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 …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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