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Showing :
Limma
•
reset
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
10 days ago • updated 10 hours ago
Chris
• 0
3
votes
4
replies
126
views
Help with error using camera() in limma
CAMERA
limma
22 hours ago • updated 17 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 18 hours 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 18 hours ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
3
replies
183
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 20 hours ago by
James W. MacDonald
65k • written 1 day 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 21 hours ago
Chris
• 0
0
votes
7
replies
284
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
14 days ago • updated 8 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 8 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
0
votes
1
reply
128
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
taur.vil
• 0
0
votes
2
replies
188
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
11 days ago • updated 9 days ago
catv
• 0
3
votes
1
reply
153
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
Shaimaa Gamal
• 0
5
votes
9
replies
892
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
20 days ago • updated 12 days ago
Chris
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 13 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
4
replies
588
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 14 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
1
vote
3
replies
337
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 16 days ago by
Gordon Smyth
50k • written 21 days ago by
Simran
• 0
2
votes
6
replies
378
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
22 days ago
Chris
• 0
0
votes
4
replies
298
views
Help with design.matrix
limma
25 days ago • updated 24 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
155
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 25 days ago by
Gordon Smyth
50k • written 25 days ago by
avery
• 0
1
vote
4
replies
423
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 26 days ago by
Gordon Smyth
50k • written 28 days ago by
jari.karppinen
• 0
5
votes
25
replies
847
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 26 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
0
votes
2
replies
180
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
28 days ago • updated 27 days ago
Gimena
• 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 29 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
22 results • Page
1 of 1
Recent ...
Replies
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
James W. MacDonald
65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
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
Votes
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
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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Ian D.
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junhui.li11
• 0
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James W. MacDonald
65k
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jeffrey.maurer
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Chris
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