Showing : lmFit • reset
1
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880
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Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma lmfit R DifferentialExpression
updated 23 months ago by ★ 4.0k • written 23 months ago by • 0
2
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3
replies
1.2k
views
lmFit, continuous exposure, adjustment covariates
lmFit
updated 23 months ago by 50k • written 2.8 years ago by • 0
0
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0
replies
746
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
2.9 years ago kyleyxw • 0
3
votes
4
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1.1k
views
lmFit, number of proteins
lmFit
3.0 years ago • updated 2.8 years ago AyHi • 0
1
vote
5
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1.4k
views
Limma for proteomic data! Please Help!
limma voom lmfit ebayesfit
updated 4.0 years ago by 50k • written 4.0 years ago by • 0
4
votes
6
replies
702
views
mean log2CPM after model fit (lmFit)
limma lmFit mean expression level
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
2
votes
2
replies
880
views
design matrix and correlate variable
limma lmfit
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 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 5.3 years ago by 50k • written 5.3 years ago by ▴ 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 ★ 28k • written 5.7 years ago by • 0
1
vote
7
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1.6k
views
model.matrix from GDS data
model.matrix lmFit eBayes GEOquery limma
6.2 years ago darthratus • 0
2
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3
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1.7k
views
Differential expression of nomalised and log2 transformed data in limma
limma lmfit model.matrix differential gene expression
6.6 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 6.6 years ago by 50k • written 6.7 years ago by ▴ 10
0
votes
3
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1.2k
views
Get back to individual measures to calculate coefficients like the lmFit fucntion (limma package)
limma lmfit weight individual
7.1 years ago stephane.cauchi ▴ 10
0
votes
2
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1.3k
views
Right use of model.matrix?
limma agilent microarray lmfit model.matrix
updated 7.4 years ago by 50k • written 7.4 years ago by ▴ 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 ★ 7.9k • written 7.4 years ago by • 0
2
votes
4
replies
1.6k
views
Problem with Agilent microarray data analysis using limma package
limma agilent microarrays lmfit
updated 7.8 years ago by 50k • written 7.8 years ago by • 0
2
votes
5
replies
4.1k
views
Analysis using a linear model
lmfit
updated 8.4 years ago by 50k • written 8.4 years ago by • 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 8.7 years ago by 65k • written 8.7 years ago by ▴ 10
2
votes
2
replies
2.4k
views
limma: Using log2 fold changes as input for a linear model fit
limma logfc lmfit
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 10
2
votes
8
replies
2.2k
views
lmFit only deals with numerical values (data matrix object)?
limma lmFit
updated 9.3 years ago by 50k • written 13.0 years ago by ▴ 210
4
votes
3
replies
4.7k
views
p-values from robust linear model in LIMMA
limma lmFit
updated 9.3 years ago by 50k • written 9.9 years ago by ▴ 40
21 results • Page 1 of 1
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Comment: Multi factor design edgeR/Deseq2 by Elizabeth • 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Comment: DESeq2 setting significant p-value by Michael Love 41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded by ATpoint ★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Votes
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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