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lmFit
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1
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845
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Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma
lmfit
R
DifferentialExpression
updated 22 months ago by
ATpoint
★ 3.9k • written 22 months ago by
Dimitris
• 0
2
votes
3
replies
1.2k
views
lmFit, continuous exposure, adjustment covariates
lmFit
updated 22 months ago by
Gordon Smyth
50k • written 2.7 years ago by
AyHi
• 0
0
votes
0
replies
725
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi
limma
lmm
lmfit
dmpFinder
2.8 years ago
kyleyxw
• 0
3
votes
4
replies
1.0k
views
lmFit, number of proteins
lmFit
2.9 years ago • updated 2.7 years ago
AyHi
• 0
1
vote
5
replies
1.3k
views
Limma for proteomic data! Please Help!
limma
voom
lmfit
ebayesfit
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
sa825
• 0
4
votes
6
replies
674
views
mean log2CPM after model fit (lmFit)
limma
lmFit
mean expression level
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
anna
• 0
2
votes
2
replies
853
views
design matrix and correlate variable
limma
lmfit
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
mouton.alice
▴ 10
2
votes
2
replies
1.1k
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 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
kediggins
▴ 10
1
vote
8
replies
1.6k
views
Design matrix for regressing gene expression on a continuous variable - age
limma
lmfit
design matrix
r
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
anupriya.dalmia
• 0
1
vote
7
replies
1.5k
views
model.matrix from GDS data
model.matrix
lmFit
eBayes
GEOquery
limma
6.1 years ago
darthratus
• 0
2
votes
3
replies
1.6k
views
Differential expression of nomalised and log2 transformed data in limma
limma
lmfit
model.matrix
differential gene expression
6.5 years ago
stinehedensted
• 0
2
votes
5
replies
2.3k
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 6.5 years ago by
Gordon Smyth
50k • written 6.6 years ago by
wewolski
▴ 10
0
votes
3
replies
1.2k
views
Get back to individual measures to calculate coefficients like the lmFit fucntion (limma package)
limma
lmfit
weight
individual
7.0 years ago
stephane.cauchi
▴ 10
0
votes
2
replies
1.3k
views
Right use of model.matrix?
limma
agilent
microarray
lmfit
model.matrix
updated 7.4 years ago by
Gordon Smyth
50k • written 7.4 years ago by
Maximilian
▴ 10
4
votes
8
replies
1.8k
views
Limma for paired and unpaired analysis with adjustment for categorical and continuous variables
limma
illumina450k
lmfit
updated 7.4 years ago by
Ryan C. Thompson
★ 7.9k • written 7.4 years ago by
DSP
• 0
2
votes
4
replies
1.5k
views
Problem with Agilent microarray data analysis using limma package
limma
agilent microarrays
lmfit
updated 7.7 years ago by
Gordon Smyth
50k • written 7.7 years ago by
Jesse L.
• 0
2
votes
5
replies
4.0k
views
Analysis using a linear model
lmfit
updated 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
libya.tahani
• 0
3
votes
6
replies
2.4k
views
How to get a list of differentialy expressed genes with data from Illumina array?
limma
illumina
microarray
lmfit
differential gene expression
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
kanacska
▴ 10
2
votes
2
replies
2.3k
views
limma: Using log2 fold changes as input for a linear model fit
limma
logfc
lmfit
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
Moritz E. Beber
▴ 10
2
votes
8
replies
2.1k
views
lmFit only deals with numerical values (data matrix object)?
limma
lmFit
updated 9.2 years ago by
Gordon Smyth
50k • written 13.0 years ago by
Peter Davidsen
▴ 210
4
votes
3
replies
4.6k
views
p-values from robust linear model in LIMMA
limma
lmFit
updated 9.2 years ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
21 results • Page
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Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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