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0
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Correct creation of design matrix in limma for testing a specific comparison of interest in a microarray dataset
limma microarray design and contrast matrix
8.1 years ago svlachavas ▴ 830
8
votes
12
replies
4.2k
views
Interaction models in limma and multiple factor assessement regarding microarray statistical inference
limma microarray interaction model multiple factor design makeContrasts
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 830
2
votes
4
replies
1.9k
views
Weird error after trying to subset an microarray expression set with gene symbols from topTable function from limma
expressionset limma annotation affymetrix microarrays
updated 8.3 years ago by 25k • written 8.3 years ago by ▴ 830
1
vote
2
replies
1.9k
views
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
ComBat diagnostic plot batch effect affymetrix microarrays sva
updated 8.3 years ago by ▴ 850 • written 8.3 years ago by ▴ 830
2
votes
2
replies
2.1k
views
Error while calling function topTable() from limma R package in microarray data analysis
limma microarray a4Core topTable statistical inference
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 830
0
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0
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1.9k
views
Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasets
sva ComBat customcdf affymetrix microarrays limma
8.3 years ago svlachavas ▴ 830
0
votes
1
reply
1.3k
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Appropriate selection of DE list in limma before and after implementation of arrayWeights in conjuction with duplicateCorrelation functions
limma microarray multifactorial design duplicatecorrelation arrayweights
8.4 years ago svlachavas ▴ 830
7
votes
6
replies
3.2k
views
Interpretation of mroast gene set analysis in R and appropriate use of the function barcode plot regarding a microarray dataset
limma mroast barcodeplot KEGG gene set testing
updated 8.5 years ago by 50k • written 8.5 years ago by ▴ 830
0
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0
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1.1k
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Background correction arguments in R package GCRMA for microarray pre-processing analysis
gcrma normalization background correction microarray
8.5 years ago svlachavas ▴ 830
2
votes
10
replies
6.1k
views
Install older specific version from an R package that is on the Bioconductor Repository
Bioconductor biocLite R packages oldversion
8.5 years ago svlachavas ▴ 830
3
votes
5
replies
2.3k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview clusterProfiler KEGGpath visualization Graphviz
updated 8.5 years ago by ★ 1.6k • written 8.5 years ago by ▴ 830
3
votes
8
replies
26k
views
"Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
BiocUpgrade Rstudio Bioconductor R3.2.2
8.5 years ago svlachavas ▴ 830
4
votes
4
replies
2.5k
views
Background correction in Illumina beadchip microarrays with limma neqc function
illumina human ht-12 v4 limma background correction BeadStudio microarray
updated 8.5 years ago by 50k • written 8.5 years ago by ▴ 830
7
votes
2
replies
2.2k
views
Appropriate explanation of the methodology behind arrayWeights function from limma R package
limma arrayWeights variance sampleQuality microarray
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by ▴ 830
4
votes
8
replies
1.7k
views
Combination of duplicateCorrelation with arrayWeights to increase power for DE detection in multilevel experiments
limma duplicatecorrelation arrayweights microarray
updated 8.6 years ago by 50k • written 8.6 years ago by ▴ 830
1
vote
2
replies
1.6k
views
Possible methodologies of machine learning in R that can assimilate continuous variables along gene expression data for microarray classification
classification machinelearning microarray multivariate caret
updated 8.6 years ago by ★ 13k • written 8.6 years ago by ▴ 830
0
votes
0
replies
1.5k
views
Possible methodologies for missing value imputation of continuous variables in a data frame in R
missing data missing value imputation impute MICE bioconductor
8.6 years ago svlachavas ▴ 830
0
votes
0
replies
1.3k
views
Possible methodologies for constructing multi-level comparisons in limma
limma paired analysis multiple factor design affymetrix microarrays duplicatecorrelation
8.6 years ago svlachavas ▴ 830
18
votes
18
replies
4.8k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma batch effect ComBat differential gene expression
updated 8.6 years ago by ▴ 850 • written 8.6 years ago by ▴ 830
0
votes
1
reply
1.8k
views
Questions regarding removal and following re-installation of a specific R package using a custom library path
package installation custom library path biocLite bioconductor
8.7 years ago svlachavas ▴ 830
0
votes
0
replies
1.3k
views
Error with R package RontoTools regarding administrator issues downloading updated KEGG data
ROntoTools Rstudio bioconductor administratorIssues pathway analysis
8.7 years ago svlachavas ▴ 830
3
votes
4
replies
1.4k
views
Problem regarding the explanation of log-fold changes of individual coefficients in limma after eBayes
limma logfoldchange limma design matrix paired samples affymetrix microarrays
updated 8.7 years ago by ★ 7.9k • written 8.7 years ago by ▴ 830
11
votes
16
replies
1.8k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma multifactorial design diagnostic plots affymetrix microarrays
updated 8.7 years ago by 66k • written 8.7 years ago by ▴ 830
0
votes
0
replies
1.2k
views
Possible(validated) methodology implemented in R for integrating and analyzing clinical data with gene expression data in R
data integration clinicaldata gene expression data PET
8.7 years ago svlachavas ▴ 830
2
votes
5
replies
5.5k
views
Update R in Rstudio to specific version 3.2.1 in windows
updateR rstudio Rversion3.2.1
updated 8.7 years ago by ★ 8.2k • written 8.7 years ago by ▴ 830
0
votes
0
replies
2.6k
views
Problem with the colors in the heatmap.2 function and the color key values range
gplots heatmap.2 affymetrix microarrays color key
8.7 years ago svlachavas ▴ 830
12
votes
20
replies
2.1k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma multifactorial design design and contrast matrix affymetrix microarrays
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 830
2
votes
2
replies
2.6k
views
Correct creation of design matrix in limma regarding a multi-level experiment
limma multiple factor design affymetrix microarrays limma paired analysis
updated 8.7 years ago by 50k • written 8.7 years ago by ▴ 830
4
votes
8
replies
1.9k
views
Annotation Problem regarding double platform merged microarray eset using the inSilicoMerging R package, after differential expression analysis
inSilicoMerging doubleannotation affymetrix microarrays limma inSilicoDB
8.7 years ago svlachavas ▴ 830
2
votes
4
replies
4.4k
views
Error and questions about clustering & ploting functions in r packages cluster and mclust regarding kmeans method
cluster mclust limma clusplot kmeans
8.8 years ago svlachavas ▴ 830
18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
9.0 years ago • updated 8.8 years ago svlachavas ▴ 830
1
vote
2
replies
2.4k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
8.8 years ago svlachavas ▴ 830
1
vote
2
replies
10k
views
Use of various distance measures and clustering methods in heatmap creation
gplots heatmap.2 bioconductor pearsoncorrelation average
8.9 years ago svlachavas ▴ 830
6
votes
4
replies
4.1k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 830
0
votes
2
replies
1.4k
views
Possible construction of heatmap for clustering only genes for different treatments and not samples
heatmap.2 clustering common DEG genes bioconductor
updated 8.9 years ago by 66k • written 8.9 years ago by ▴ 830
7
votes
10
replies
1.7k
views
Possible TF binding site enrichment analysis through mroast and conversion problems
TF binding site analysis bioconductor mroast limma promoter analysis
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 830
5
votes
11
replies
1.8k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma mroast GSEA GO illumina human ht-12 v4
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 830
2
votes
2
replies
1.6k
views
Annotation problems regarding quality information for Illumina HumanHT-12 v4-illuminaHumanv4.db
illumina human ht-12 v4 illuminahumanv4.db filtering on probe annotation illumina
updated 9.0 years ago by ★ 6.5k • written 9.0 years ago by ▴ 830
1
vote
2
replies
1.4k
views
Annotation issues with illumina microarray preprocessing with limma
limma illumina human ht-12 v4 annotationdbi lumihumanAll.db lumihumanidmapping
updated 9.0 years ago by 50k • written 9.0 years ago by ▴ 830
2
votes
8
replies
3.6k
views
Problems importing Illumina raw data with lumi R package
Illumina Human HT-12 v4 lumi limma microarray
updated 9.0 years ago by 50k • written 9.0 years ago by ▴ 830
22
votes
4
replies
10.0k
views
Correct assumptions of using limma moderated t-test
limma statistical inference variance test bioconductor
updated 9.0 years ago by 50k • written 9.0 years ago by ▴ 830
6
votes
10
replies
1.8k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing roast mroast differential gene expression bioconductor
9.0 years ago svlachavas ▴ 830
2
votes
3
replies
2.8k
views
Questions in limma about multifactorial design and possible batch effect correction
limma batcheffect batcheffectcorrection multiple factor design
updated 9.0 years ago by 66k • written 9.0 years ago by ▴ 830
0
votes
1
reply
2.4k
views
Error while trying to upgrade R to version 3.2
bioconductor upgrade installr Windows8 R 3.2
9.1 years ago svlachavas ▴ 830
0
votes
0
replies
1.4k
views
Error in R package "cancerclass" with function nvalidate
cancerclass bioconductor machinelearning classification
9.1 years ago svlachavas ▴ 830
0
votes
0
replies
1.6k
views
Machine learning methods for feature selection and possible correlation with clinical data
machinelearning clinicaldata biomarkers data integration bioconductor
9.1 years ago svlachavas ▴ 830
2
votes
16
replies
2.7k
views
Possible ways of performing non-specific intensity filtering on Perfect-match only affymetrix array
oligo DABG non-specific filtering primeview
9.1 years ago svlachavas ▴ 830
0
votes
0
replies
1.2k
views
Possible implementation of two class paired Rank Products in r with package RankProd
RankProd pairedtest bioconductor biologicalreplicates
9.1 years ago svlachavas ▴ 830
1
vote
5
replies
1.9k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma bioconductor batcheffect Primeview insilicomerging
updated 9.1 years ago by ▴ 830 • written 9.1 years ago by ▴ 830
0
votes
0
replies
1.2k
views
Correst use of GeneOverlap R Package
GeneOverlap DEGgenes affymetrixchip bioconductor
9.1 years ago svlachavas ▴ 830
121 results • Page 2 of 3
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