Showing : lmfit • reset
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
8
replies
2.2k
views
lmFit only deals with numerical values (data matrix object)?
limma lmFit
updated 9.3 years ago by 50k • written 13.1 years ago by ▴ 210
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
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
2
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4
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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
0
votes
2
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1.3k
views
Right use of model.matrix?
limma agilent microarray lmfit model.matrix
updated 7.5 years ago by 50k • written 7.5 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 7.5 years ago by ★ 7.9k • written 7.5 years ago by • 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
2
votes
3
replies
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
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
1
vote
8
replies
1.6k
views
Design matrix for regressing gene expression on a continuous variable - age
limma lmfit design matrix r
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
2
votes
2
replies
889
views
design matrix and correlate variable
limma lmfit
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
4
votes
6
replies
711
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
1
vote
5
replies
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
2
votes
3
replies
1.3k
views
lmFit, continuous exposure, adjustment covariates
lmFit
updated 23 months ago by 50k • written 2.8 years ago by • 0
1
vote
1
reply
892
views
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
3
votes
4
replies
1.1k
views
lmFit, number of proteins
lmFit
3.0 years ago • updated 2.8 years ago AyHi • 0
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
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
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
0
votes
0
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755
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Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
2.9 years ago kyleyxw • 0
21 results • Page 1 of 1
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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