Showing : glad • reset
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DiffBind (Please add me to the Dropbox containing the vignette data)
GLAD edgeR DiffBind DESeq2 GLAD edgeR DiffBind DESeq2
10.8 years ago Rory Stark ★ 5.2k
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1.1k
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Limma design : What is the
GLAD GLAD
10.8 years ago Santy Marques-Ladeira ▴ 20
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3
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1.4k
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GLAD crashes when built with gcc-4.8
GLAD GLAD
updated 11.0 years ago by 25k • written 11.0 years ago by ▴ 70
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865
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arrayQualityMetrics does not produce interactive plots
GLAD GLAD
11.0 years ago Wolfgang Huber ★ 13k
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makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
11.3 years ago Sarah Pohl ▴ 30
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3
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2.2k
views
Diffbind: Binding Affinity Heatmap
Sequencing GO Clustering GLAD edgeR DESeq DiffBind Sequencing GO Clustering GLAD edgeR
11.4 years ago Rory Stark ★ 5.2k
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1
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1.1k
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beadarray library: perBeadFile
GLAD beadarray GLAD beadarray
updated 11.4 years ago by ★ 6.6k • written 11.4 years ago by ▴ 10
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1
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1.8k
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Issue of installing the GLAD package
GLAD GLAD
updated 11.5 years ago by 1.6k • written 11.5 years ago by ★ 13k
1
vote
1
reply
2.3k
views
multiple threads on QuasR
Alignment GLAD QuasR Alignment GLAD QuasR
11.7 years ago Michael Stadler ▴ 350
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1.0k
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rhdf5 and factors
GO GLAD GO GLAD
11.9 years ago Stephen Eglen ▴ 10
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3
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1.9k
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Merging various panel for flow cytometry
GLAD flowCore flowViz GLAD flowCore flowViz
updated 12.1 years ago by ★ 1.3k • written 12.1 years ago by ▴ 160
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0
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971
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question on easyRNASeq developer version
GLAD easyRNASeq GLAD easyRNASeq
12.2 years ago delhomme@embl.de ★ 1.2k
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2
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1.6k
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DESeq - Estimating Dispersion with Technical Replicates
GLAD DESeq GLAD DESeq
updated 12.3 years ago by ★ 13k • written 12.3 years ago by ▴ 20
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0
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1.3k
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question regarding ChIPPeakAnno use
Annotation annotate GLAD ChIPpeakAnno Annotation annotate GLAD ChIPpeakAnno
12.3 years ago Julie Zhu ★ 4.3k
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1.2k
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HTqPCR problems
Microarray qPCR GO Preprocessing GLAD HTqPCR Microarray qPCR GO Preprocessing GLAD
12.3 years ago cfischer ▴ 10
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918
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(no subject)
Clustering probe limma GLAD Clustering probe limma GLAD
12.4 years ago Gordon Smyth 52k
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4
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1.7k
views
HTqPCR problems
qPCR GO Preprocessing GLAD HTqPCR qPCR GO Preprocessing GLAD HTqPCR
updated 12.5 years ago by ▴ 340 • written 12.5 years ago by ★ 2.0k
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6
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2.4k
views
HTqPCR
qPCR GO GLAD HTqPCR qPCR GO GLAD HTqPCR
updated 12.5 years ago by ★ 2.0k • written 12.5 years ago by ▴ 40
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13
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2.2k
views
PWMscoreStartingAt and ambiguous subject seqs
Cancer Biostrings GLAD Cancer Biostrings GLAD
updated 12.6 years ago by 16k • written 12.6 years ago by ▴ 740
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2.7k
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gene set enrichment analysis of RNA-Seq data
Microarray limma GLAD edgeR goseq Microarray limma GLAD edgeR goseq
12.6 years ago Paolo Guarnieri ▴ 20
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Fwd: RCytoscape couldn't connect to host
GO GLAD RCytoscape GO GLAD RCytoscape
12.7 years ago Paul Shannon ▴ 750
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1.3k
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[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
12.9 years ago Valerie Obenchain ★ 6.8k
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1
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1.7k
views
Rgraphviz installing problem
Rgraphviz GLAD Rgraphviz GLAD
updated 12.9 years ago by 25k • written 12.9 years ago by ▴ 10
0
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1
reply
972
views
[Rocky] - LIMMA to identify deferentially expressed genes
affy limma GLAD affy limma GLAD
updated 12.9 years ago by 21k • written 12.9 years ago by ▴ 30
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0
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1.0k
views
edgeR - R script - results compared to DESeq
GLAD edgeR DESeq GLAD edgeR DESeq
13.1 years ago Gordon Smyth 52k
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2
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1.5k
views
error in loading GLAD package
GLAD GLAD
updated 13.1 years ago by 25k • written 13.1 years ago by ▴ 110
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1
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1.7k
views
[Bioc-sig-seq] as.data.frame on GRanges object with DNAStringSet in values
Cancer Biostrings GLAD Cancer Biostrings GLAD
updated 13.2 years ago by ★ 11k • written 13.2 years ago by 16k
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1.6k
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I: R: R: R: Probe-level analysis of exon arrays using xps
Annotation Normalization Preprocessing Breast Prostate probe GLAD Category xps Annotation
13.3 years ago Lavorgna Giovanni ▴ 80
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2
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957
views
Help with the weaver example from limma package
Annotation GLAD Annotation GLAD
updated 13.5 years ago by 52k • written 13.5 years ago by ▴ 20
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1
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1.0k
views
Rgraphviz windows version incompatible with current Graphviz
Rgraphviz PROcess GLAD Rgraphviz PROcess GLAD
updated 13.6 years ago by 25k • written 13.6 years ago by ▴ 10
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1
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1.5k
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how to do paired t-tests for multiple subgroups [was: warnings or potential problems in limma procedure]
Cancer limma GLAD Category Cancer limma GLAD Category
updated 13.7 years ago by ▴ 100 • written 13.7 years ago by 52k
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1
reply
1.5k
views
edgeR glm fit error
GO GLAD edgeR GO GLAD edgeR
13.8 years ago Gordon Smyth 52k
0
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1
reply
950
views
Newbie question
GLAD GLAD
updated 13.9 years ago by 67k • written 13.9 years ago by ▴ 30
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1
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1.6k
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[Rocky] - Clarification for finding SNPs at 3'UTR, 5'UTR, CDS genomic regions
SNP Cancer GLAD SNP Cancer GLAD
updated 14.0 years ago by 16k • written 14.0 years ago by ▴ 30
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2
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2.4k
views
problem installing 'GLAD' package
cdf GLAD cdf GLAD
14.1 years ago Shenglin Zheng ▴ 20
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975
views
HTqPCR question
Microarray limma GLAD HTqPCR Microarray limma GLAD HTqPCR
14.1 years ago Heidi Dvinge ★ 2.0k
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1.3k
views
error in plotKEGGGraph
Pathways GLAD KEGGgraph Pathways GLAD KEGGgraph
14.2 years ago Robert M. Flight ▴ 280
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1
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1.4k
views
write.XStringView/write.XStringSet highly inefficient (solved)
Cancer BSgenome PROcess GLAD BSgenome Cancer BSgenome PROcess GLAD BSgenome
updated 14.4 years ago by ★ 13k • written 14.4 years ago by ▴ 550
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1
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1.8k
views
Design matrix for time course analysis with maSigPro
GLAD maSigPro GLAD maSigPro
updated 14.6 years ago by ★ 13k • written 14.6 years ago by ▴ 10
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4
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1.3k
views
Discrepancy on results from gcrma function and justGCRMA
gcrma GLAD gcrma GLAD
updated 14.9 years ago by 67k • written 14.9 years ago by ★ 2.0k
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4
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1.6k
views
Positive correlation between dye-swap technical replicates
Normalization Clustering probe limma GLAD Normalization Clustering probe limma GLAD
14.9 years ago Michał Góralski ▴ 40
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13
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2.0k
views
problem with data processing in R
PROcess GLAD PROcess GLAD
updated 15.0 years ago by ★ 1.7k • written 15.0 years ago by ▴ 170
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7
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1.7k
views
problem to compute copy number with crlmm
GLAD crlmm GLAD crlmm
updated 15.1 years ago by ▴ 250 • written 15.1 years ago by ▴ 40
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0
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1.2k
views
general CGH threshold question
aCGH CGH aCGH GLAD snapCGH aCGH CGH aCGH GLAD snapCGH
15.3 years ago Wolfgang RAFFELSBERGER ▴ 140
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0
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5.4k
views
Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
15.4 years ago Michael Dondrup ▴ 140
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4
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3.4k
views
retrieving mRNA sequences via biomaRt
GLAD biomaRt GLAD biomaRt
updated 15.4 years ago by ★ 13k • written 15.4 years ago by ▴ 30
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1
reply
1.3k
views
Normalized data in expresso and Expression Console differ
Normalization GLAD Normalization GLAD
updated 15.5 years ago by ★ 3.9k • written 15.5 years ago by ▴ 10
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0
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1.2k
views
browseGenome width question (rtracklayer)
Epigenetics GO hgu95av2 GLAD rtracklayer Epigenetics GO hgu95av2 GLAD rtracklayer
15.9 years ago Michael Lawrence ▴ 620
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0
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1.9k
views
getSeq human genomic sequences
Annotation Cancer BSgenome PROcess GLAD BSgenome IRanges Annotation Cancer BSgenome GLAD
15.9 years ago Hervé Pagès 16k
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2
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1.4k
views
Problem with Annotation of Mouse4302.db in simpleaffy
Annotation mouse4302 simpleaffy GLAD Annotation mouse4302 simpleaffy GLAD
updated 15.9 years ago by 67k • written 15.9 years ago by ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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Scholar to James W. MacDonald 67k
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