0
votes
1
reply
1.4k
views
Questions about the correct implementation of the function plotRLDF from R package limma regarding classification of a microarray dataset
limma microarray plotRLDF classification
9.6 years ago svlachavas ▴ 840
1
vote
3
replies
2.4k
views
Bioc 3.3 Windows 10 eiR package fails to install
software error R cheminformatics package installation eiR
updated 9.6 years ago by ▴ 10 • written 9.6 years ago by • 0
4
votes
5
replies
1.8k
views
parRapply in BiocParallel ?
biocparallel variantannotation
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 350
3
votes
2
replies
2.3k
views
Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
snprelate GWASTools
updated 9.6 years ago by ▴ 30 • written 9.6 years ago by ▴ 40
1
vote
7
replies
1.9k
views
Biomart: listMarts, listFilters and listAttributes work, but getBM doesn't
biomart
updated 9.6 years ago by 68k • written 9.6 years ago by • 0
0
votes
3
replies
3.2k
views
Annotation in ExpressionSet object
ExpressionSet globaltest
9.6 years ago NS ▴ 60
1
vote
3
replies
1.7k
views
VennDiagram from two TestResults matrices
limma venn diagram
updated 9.6 years ago by 53k • written 9.6 years ago by ▴ 10
0
votes
0
replies
1.5k
views
plotting normalized RPM coverage for plus and minus strands in gviz
gviz rsamtools
9.6 years ago amias ▴ 10
1
vote
5
replies
2.4k
views
Error using Rsubread align: caugh segfault invalid permissions
rsubread align segfault
updated 9.6 years ago by ★ 3.6k • written 9.6 years ago by ▴ 10
9
votes
6
replies
4.5k
views
about paired-samples in edgeR
edger
9.6 years ago Bogdan ▴ 670
0
votes
1
reply
1.3k
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 9.6 years ago by ★ 29k • written 9.6 years ago by • 0
1
vote
4
replies
2.6k
views
DESeq2 "results" Error in .classEnv(classDef)
deseq2
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
2
votes
25
replies
8.5k
views
How to use Limma to analyze differences among group items without doing pairwise comparisons
limma
9.7 years ago • updated 9.6 years ago sami.pietila • 0
2
votes
6
replies
3.9k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 9.6 years ago by ▴ 90
0
votes
0
replies
2.0k
views
methyAnalysis error with example data
methyanalysis
9.6 years ago Tom ▴ 10
1
vote
4
replies
1.8k
views
Error using countBam (Rsamtools package)
rsamtools countbam
9.6 years ago t.kuilman ▴ 170
0
votes
0
replies
1.0k
views
How to calculate risk of relapse based on subtypes and proliferation (ROR-P) PAM50 sub-typing?
RORP PAM50
9.6 years ago g_draculla ▴ 10
0
votes
3
replies
2.0k
views
Trouble with Custom PC Plot
deseq2 plotPCA PCA rna-seq
9.6 years ago newsomew13 • 0
0
votes
1
reply
955
views
question for SVA package
getting error in gsva function
updated 9.6 years ago by ▴ 650 • written 9.6 years ago by • 0
5
votes
4
replies
2.1k
views
Is there a way to remove or take the first overlapping gene(s) when using makeTxDbFromGFF?
genomicfeatures
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 40
1
vote
1
reply
2.4k
views
Null model in SVA for patient paired test comparing tumor vs normal
sva paired samples rnaseq
updated 9.6 years ago by ▴ 650 • written 9.6 years ago by • 0
0
votes
6
replies
3.1k
views
EBImage readImage hangs when reading tif file with multiple frames.
software error ebimage
updated 9.6 years ago by ▴ 750 • written 9.7 years ago by • 0
0
votes
1
reply
1.2k
views
[VariantAnnotation] Unable to set a genotype with geno()
variantannotation
updated 9.6 years ago by 4.3k • written 9.6 years ago by • 0
1
vote
6
replies
1.8k
views
Are these contrasts correct for use in DESeq2?
deseq2 contrast
updated 9.6 years ago by 43k • written 9.6 years ago by ▴ 90
6
votes
4
replies
2.2k
views
Clarification on DESeq2 normalizationFactors(), estimateDispersions() and varianceStabilizingTransformation()
deseq2
updated 9.6 years ago by 43k • written 9.6 years ago by ▴ 680
5
votes
7
replies
2.6k
views
Gviz: How to plot UTRs with GRanges object?
gviz
updated 9.6 years ago by ★ 1.6k • written 9.7 years ago by ▴ 90
2
votes
5
replies
2.8k
views
Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
gviz bam pacbio
updated 9.6 years ago by ★ 1.6k • written 9.7 years ago by • 0
0
votes
0
replies
1.3k
views
[EBSeq] Normalization and DE genes detection
ebseq normalization differential gene expression
9.6 years ago jean.keller ▴ 10
0
votes
6
replies
5.5k
views
Nonexistent include directory
software error r package problem
updated 9.6 years ago by 25k • written 9.6 years ago by • 0
4
votes
5
replies
7.1k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 9.6 years ago by ★ 3.6k • written 9.7 years ago by ▴ 180
5
votes
2
replies
13k
views
lowess vs. loess
Microarray Normalization
updated 9.6 years ago by 53k • written 22.4 years ago by ▴ 30
1
vote
1
reply
955
views
hom.Hs.inp_dbschema of the Inparanoid annotation package not working properly
software error annotationdbi
updated 9.6 years ago by 16k • written 9.6 years ago by • 0
2
votes
2
replies
1.6k
views
taking intersection between 6 networks by graph.intersect
igraph software error adjacency matrix
updated 9.6 years ago by ▴ 470 • written 9.7 years ago by ▴ 40
3
votes
1
reply
1.5k
views
parsing flowFrame@description in flowCore
FCS file flowcore @description
updated 9.6 years ago by ★ 1.3k • written 9.6 years ago by ▴ 70
1
vote
3
replies
2.1k
views
limma overfitting model due to intercept and yet exclusion of intercept= uninterpretable results
limma microarray linear model statistical modeling model.matrix
9.6 years ago christopher.clarskon15 ▴ 20
0
votes
1
reply
1.7k
views
ggbio OrganismDb autoplot - reduce vs identity
ggbio autoplot
updated 9.6 years ago by 68k • written 9.7 years ago by ▴ 380
0
votes
0
replies
1.5k
views
AnnotationData Packages version and pipeline management
docker annotation pipeline
9.6 years ago Elena Grassi ▴ 10
3
votes
10
replies
2.8k
views
Combining data from multiple illumina microarray experiments
normalization limma
updated 9.6 years ago by 53k • written 9.6 years ago by ▴ 420
0
votes
3
replies
1.8k
views
DiffBind dba.count() seqfault
diffbind dba.count
9.6 years ago em540 • 0
0
votes
1
reply
1.0k
views
DESeq erroneously normalizing all values to mean of one specific variable - what's wrong?
deseq2 normalization fitType parametric
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
4
votes
5
replies
1.8k
views
XStringSet operations discard names - how to address?
biostrings
updated 9.6 years ago by 16k • written 9.7 years ago by • 0
2
votes
6
replies
7.1k
views
PCA in DESeq2 - Can I get the genes contributing most to each component?
deseq2 pca
9.7 years ago Emily ▴ 10
2
votes
2
replies
2.7k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2 rnaseq contrast multiple comparisons fdrtool
9.7 years ago sebastiano.curreli • 0
5
votes
12
replies
6.3k
views
Differential expression analysis: comparison of DESeq2 and edgeR robust results
deseq2 edgeR differential gene expression
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 90
4
votes
2
replies
5.0k
views
DESeq2 color coding
DESeq2 color R package
updated 9.7 years ago by ★ 6.6k • written 9.7 years ago by • 0
6
votes
11
replies
2.9k
views
microarray data analsis with limma?
limma genepix microarray agilent microarrays
9.7 years ago Mehmet Ilyas Cosacak • 0
3
votes
3
replies
2.4k
views
pairwiseAlignments coordinate mapping?
biostrings pairwisealignment
updated 8 months ago by ▴ 20 • written 9.7 years ago by ★ 13k
2
votes
1
reply
2.3k
views
GEOquery::getGEO warning: not all columns named in 'colClasses' exist
GEOquery
updated 9.7 years ago by 21k • written 9.7 years ago by ▴ 110
4
votes
5
replies
1.5k
views
DESeq2 how to define my conditions when I want the results comparing a subset of samples
deseq2 rnaseq
updated 9.7 years ago by ★ 7.9k • written 9.7 years ago by ▴ 10
0
votes
1
reply
1.2k
views
offTargetAnalysis result interpretation
crisprseek
updated 9.7 years ago by ★ 4.3k • written 9.7 years ago by • 0
46,711 results • Page 394 of 935
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