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lmfit
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404
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Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma
lmfit
R
DifferentialExpression
updated 8 months ago by
ATpoint
★ 2.1k • written 8 months ago by
Dimitris
• 0
2
votes
3
replies
635
views
lmFit, continuous exposure, adjustment covariates
lmFit
updated 8 months ago by
Gordon Smyth
47k • written 19 months ago by
AyHi
• 0
0
votes
0
replies
404
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi
limma
lmm
lmfit
dmpFinder
20 months ago
kyleyxw
• 0
3
votes
4
replies
638
views
lmFit, number of proteins
lmFit
21 months ago • updated 19 months ago
AyHi
• 0
1
vote
5
replies
712
views
Limma for proteomic data! Please Help!
limma
voom
lmfit
ebayesfit
updated 2.8 years ago by
Gordon Smyth
47k • written 2.8 years ago by
sa825
• 0
4
votes
6
replies
357
views
mean log2CPM after model fit (lmFit)
limma
lmFit
mean expression level
updated 2.9 years ago by
James W. MacDonald
62k • written 2.9 years ago by
anna
• 0
2
votes
2
replies
516
views
design matrix and correlate variable
limma
lmfit
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
mouton.alice
▴ 10
2
votes
2
replies
716
views
Different results from limma depending on whether or not I have an intercept term in my model
limma
lmfit
voom
limma design matrix
voomwithqualityweights
updated 4.1 years ago by
Gordon Smyth
47k • written 4.1 years ago by
kediggins
▴ 10
0
votes
8
replies
956
views
Design matrix for regressing gene expression on a continuous variable - age
limma
lmfit
design matrix
r
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
anupriya.dalmia
• 0
1
vote
7
replies
1.0k
views
model.matrix from GDS data
model.matrix
lmFit
eBayes
GEOquery
limma
5.0 years ago
darthratus
• 0
2
votes
3
replies
1.1k
views
Differential expression of nomalised and log2 transformed data in limma
limma
lmfit
model.matrix
differential gene expression
5.4 years ago
stinehedensted
• 0
2
votes
5
replies
1.8k
views
Why does limma contrast.fit produces NA's for all contrast although missing data only in one condition?
limma
contrast
missing data
lmfit
makecontrasts
updated 5.4 years ago by
Gordon Smyth
47k • written 5.5 years ago by
wewolski
▴ 10
0
votes
3
replies
884
views
Get back to individual measures to calculate coefficients like the lmFit fucntion (limma package)
limma
lmfit
weight
individual
5.9 years ago
stephane.cauchi
▴ 10
0
votes
2
replies
940
views
Right use of model.matrix?
limma
agilent
microarray
lmfit
model.matrix
updated 6.2 years ago by
Gordon Smyth
47k • written 6.2 years ago by
Maximilian
▴ 10
4
votes
8
replies
1.4k
views
Limma for paired and unpaired analysis with adjustment for categorical and continuous variables
limma
illumina450k
lmfit
updated 6.2 years ago by
Ryan C. Thompson
7.8k • written 6.2 years ago by
DSP
• 0
2
votes
4
replies
1.1k
views
Problem with Agilent microarray data analysis using limma package
limma
agilent microarrays
lmfit
updated 6.6 years ago by
Gordon Smyth
47k • written 6.6 years ago by
Jesse L.
• 0
2
votes
5
replies
3.2k
views
Analysis using a linear model
lmfit
updated 7.2 years ago by
Gordon Smyth
47k • written 7.2 years ago by
libya.tahani
• 0
3
votes
6
replies
1.8k
views
How to get a list of differentialy expressed genes with data from Illumina array?
limma
illumina
microarray
lmfit
differential gene expression
updated 7.5 years ago by
James W. MacDonald
62k • written 7.5 years ago by
kanacska
▴ 10
2
votes
2
replies
1.9k
views
limma: Using log2 fold changes as input for a linear model fit
limma
logfc
lmfit
updated 7.7 years ago by
Aaron Lun
★ 28k • written 7.7 years ago by
Moritz E. Beber
▴ 10
2
votes
8
replies
1.7k
views
lmFit only deals with numerical values (data matrix object)?
limma
lmFit
updated 8.1 years ago by
Gordon Smyth
47k • written 11.8 years ago by
Peter Davidsen
▴ 210
4
votes
3
replies
4.0k
views
p-values from robust linear model in LIMMA
limma
lmFit
updated 8.1 years ago by
Gordon Smyth
47k • written 8.7 years ago by
Arvid Sondén
▴ 40
21 results • Page
1 of 1
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Replies
Comment: TCGA: clinical data and expression data
by
sharifnstu1203002m
• 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Jonathan Göke
▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
by
Gordon Smyth
47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user)
by
lalanis1
• 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma
by
Gordon Smyth
47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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James W. MacDonald
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39k
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Gordon Smyth
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Bogdan
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