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6
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19
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 10 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 10 hours ago
Chris
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 7 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 4 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 7 hours ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 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 9 hours ago by
James W. MacDonald
65k • written 1 day ago by
SSSJec
• 0
0
votes
3
replies
144
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 10 hours ago by
Alejandro Reyes
★ 1.9k • written 12 days ago by
Alessia
• 0
3
votes
4
replies
101
views
Help with error using camera() in limma
CAMERA
limma
10 hours ago • updated 6 hours ago
Chris
• 0
0
votes
1
reply
84
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 7 hours ago by
James W. MacDonald
65k • written 22 hours ago by
SSSJec
• 0
0
votes
1
reply
51
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 12 hours ago by
Michael Love
41k • written 1 day ago by
Agung
• 0
0
votes
1
reply
48
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 12 hours ago by
Michael Love
41k • written 18 hours ago by
Aurora
• 0
0
votes
1
reply
46
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 12 hours ago by
Michael Love
41k • written 13 hours ago by
marcusn
• 0
0
votes
1
reply
43
views
putting my own expression data in deseq2
DESeq2
updated 15 hours ago by
ATpoint
★ 4.1k • written 16 hours ago by
Dev
• 0
0
votes
1
reply
40
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 13 hours ago by
shepherl
3.8k • written 21 hours ago by
bounlu
• 0
0
votes
0
replies
21
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
13 hours ago
Maria Doyle
▴ 70
0
votes
0
replies
14
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
3 hours ago
HAK
• 0
0
votes
0
replies
9
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
1 hour ago • updated 48 minutes ago
Yveto
• 0
17 results • Page
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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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