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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 7 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 7 hours ago
Chris
• 0
8
votes
5
replies
1.6k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Sara
• 0 • 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 5 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 2 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 5 hours ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
1
vote
3
replies
834
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
353
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
9 days ago • updated 6 days ago
fernanda.backsouza
▴ 10
2
votes
9
replies
327
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
309
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
3
votes
1
reply
278
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
i.sudbery
▴ 40
0
votes
5
replies
277
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
274
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
255
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
225
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
209
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
2
votes
5
replies
204
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
187
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
181
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
169
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 7 hours ago by
James W. MacDonald
65k • written 1 day ago by
SSSJec
• 0
1
vote
3
replies
168
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 4 days ago by
Michael Love
41k • written 5 days ago by
JalapenoCornbread
• 0
3
votes
3
replies
168
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 1 day ago by
bioinf
▴ 10
0
votes
2
replies
161
views
PCA plot suggestions
DESeq2
PCAtools
updated 4 days ago by
Michael Love
41k • written 5 days ago by
Aaliya
• 0
0
votes
3
replies
144
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 hours ago by
Alejandro Reyes
★ 1.9k • written 12 days ago by
Alessia
• 0
1
vote
1
reply
138
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
131
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
127
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
116
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
0
votes
1
reply
97
views
ATACseq merge peaks
DiffBind
updated 4 days ago by
ATpoint
★ 4.1k • written 6 days ago by
Shloka
• 0
1
vote
1
reply
95
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
3
votes
4
replies
94
views
Help with error using camera() in limma
CAMERA
limma
8 hours ago • updated 3 hours ago
Chris
• 0
0
votes
1
reply
75
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 5 hours ago by
James W. MacDonald
65k • written 20 hours ago by
SSSJec
• 0
0
votes
0
replies
64
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
62
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
6 days ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
59
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
6 days ago • updated 1 day ago
Sara
• 0
0
votes
1
reply
49
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 9 hours ago by
Michael Love
41k • written 1 day ago by
Agung
• 0
0
votes
1
reply
47
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 10 hours ago by
Michael Love
41k • written 16 hours ago by
Aurora
• 0
0
votes
1
reply
46
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 9 hours ago by
Michael Love
41k • written 10 hours ago by
marcusn
• 0
0
votes
1
reply
41
views
putting my own expression data in deseq2
DESeq2
updated 13 hours ago by
ATpoint
★ 4.1k • written 14 hours ago by
Dev
• 0
0
votes
1
reply
40
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 11 hours ago by
shepherl
3.8k • written 19 hours ago by
bounlu
• 0
0
votes
0
replies
34
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
20
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
10 hours ago
Maria Doyle
▴ 70
0
votes
0
replies
12
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
1 hour ago
HAK
• 0
45 results • Page
1 of 1
Recent ...
Replies
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 …
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. …
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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