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
10.1 years ago Rory Stark ★ 5.2k
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916
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Limma design : What is the
GLAD GLAD
10.2 years ago Santy Marques-Ladeira ▴ 20
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3
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1.3k
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GLAD crashes when built with gcc-4.8
GLAD GLAD
updated 10.4 years ago by 25k • written 10.4 years ago by ▴ 70
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768
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arrayQualityMetrics does not produce interactive plots
GLAD GLAD
10.4 years ago Wolfgang Huber ★ 13k
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makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
10.7 years ago Sarah Pohl ▴ 30
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3
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2.0k
views
Diffbind: Binding Affinity Heatmap
Sequencing GO Clustering GLAD edgeR DESeq DiffBind Sequencing GO Clustering GLAD edgeR
10.7 years ago Rory Stark ★ 5.2k
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1
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1.0k
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beadarray library: perBeadFile
GLAD beadarray GLAD beadarray
updated 10.7 years ago by ★ 6.5k • written 10.8 years ago by ▴ 10
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1
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1.7k
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Issue of installing the GLAD package
GLAD GLAD
updated 10.9 years ago by 1.6k • written 10.9 years ago by ★ 13k
1
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1
reply
2.0k
views
multiple threads on QuasR
Alignment GLAD QuasR Alignment GLAD QuasR
11.1 years ago • updated 11.0 years ago Michael Stadler ▴ 350
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924
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rhdf5 and factors
GO GLAD GO GLAD
11.3 years ago Stephen Eglen ▴ 10
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3
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1.6k
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Merging various panel for flow cytometry
GLAD flowCore flowViz GLAD flowCore flowViz
updated 11.4 years ago by ★ 1.3k • written 11.4 years ago by ▴ 160
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859
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question on easyRNASeq developer version
GLAD easyRNASeq GLAD easyRNASeq
11.6 years ago delhomme@embl.de ★ 1.2k
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2
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1.5k
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DESeq - Estimating Dispersion with Technical Replicates
GLAD DESeq GLAD DESeq
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 20
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question regarding ChIPPeakAnno use
Annotation annotate GLAD ChIPpeakAnno Annotation annotate GLAD ChIPpeakAnno
11.6 years ago Julie Zhu ★ 4.3k
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HTqPCR problems
Microarray qPCR GO Preprocessing GLAD HTqPCR Microarray qPCR GO Preprocessing GLAD
11.7 years ago cfischer ▴ 10
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818
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(no subject)
Clustering probe limma GLAD Clustering probe limma GLAD
11.7 years ago Gordon Smyth 50k
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4
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1.4k
views
HTqPCR problems
qPCR GO Preprocessing GLAD HTqPCR qPCR GO Preprocessing GLAD HTqPCR
updated 11.8 years ago by ▴ 340 • written 11.8 years ago by ★ 2.0k
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6
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2.2k
views
HTqPCR
qPCR GO GLAD HTqPCR qPCR GO GLAD HTqPCR
updated 11.9 years ago by ★ 2.0k • written 11.9 years ago by ▴ 40
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13
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1.9k
views
PWMscoreStartingAt and ambiguous subject seqs
Cancer Biostrings GLAD Cancer Biostrings GLAD
updated 12.0 years ago by 16k • written 12.0 years ago by ▴ 740
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2.6k
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gene set enrichment analysis of RNA-Seq data
Microarray limma GLAD edgeR goseq Microarray limma GLAD edgeR goseq
12.0 years ago Paolo Guarnieri ▴ 20
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1.1k
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Fwd: RCytoscape couldn't connect to host
GO GLAD RCytoscape GO GLAD RCytoscape
12.0 years ago Paul Shannon ▴ 750
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1.2k
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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
12.3 years ago Valerie Obenchain ★ 6.8k
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1
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1.6k
views
Rgraphviz installing problem
Rgraphviz GLAD Rgraphviz GLAD
updated 12.3 years ago by 25k • written 12.3 years ago by ▴ 10
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1
reply
868
views
[Rocky] - LIMMA to identify deferentially expressed genes
affy limma GLAD affy limma GLAD
updated 12.3 years ago by 21k • written 12.3 years ago by ▴ 30
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0
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946
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edgeR - R script - results compared to DESeq
GLAD edgeR DESeq GLAD edgeR DESeq
12.4 years ago Gordon Smyth 50k
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2
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1.4k
views
error in loading GLAD package
GLAD GLAD
updated 12.5 years ago by 25k • written 12.5 years ago by ▴ 110
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1
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1.6k
views
[Bioc-sig-seq] as.data.frame on GRanges object with DNAStringSet in values
Cancer Biostrings GLAD Cancer Biostrings GLAD
updated 12.6 years ago by ★ 11k • written 12.6 years ago by 16k
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1.5k
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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
12.6 years ago Lavorgna Giovanni ▴ 80
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2
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842
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Help with the weaver example from limma package
Annotation GLAD Annotation GLAD
updated 12.9 years ago by 50k • written 12.9 years ago by ▴ 20
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1
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879
views
Rgraphviz windows version incompatible with current Graphviz
Rgraphviz PROcess GLAD Rgraphviz PROcess GLAD
updated 13.0 years ago by 25k • written 13.0 years ago by ▴ 10
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1
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1.3k
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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 13.1 years ago by ▴ 100 • written 13.1 years ago by 50k
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1
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1.3k
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edgeR glm fit error
GO GLAD edgeR GO GLAD edgeR
13.2 years ago Gordon Smyth 50k
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1
reply
846
views
Newbie question
GLAD GLAD
updated 13.3 years ago by 65k • written 13.3 years ago by ▴ 30
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1
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1.4k
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[Rocky] - Clarification for finding SNPs at 3'UTR, 5'UTR, CDS genomic regions
SNP Cancer GLAD SNP Cancer GLAD
updated 13.3 years ago by 16k • written 13.3 years ago by ▴ 30
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2
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2.2k
views
problem installing 'GLAD' package
cdf GLAD cdf GLAD
13.4 years ago Shenglin Zheng ▴ 20
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877
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HTqPCR question
Microarray limma GLAD HTqPCR Microarray limma GLAD HTqPCR
13.5 years ago Heidi Dvinge ★ 2.0k
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1.2k
views
error in plotKEGGGraph
Pathways GLAD KEGGgraph Pathways GLAD KEGGgraph
13.6 years ago Robert M. Flight ▴ 280
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1
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1.3k
views
write.XStringView/write.XStringSet highly inefficient (solved)
Cancer BSgenome PROcess GLAD BSgenome Cancer BSgenome PROcess GLAD BSgenome
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ▴ 550
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1
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1.6k
views
Design matrix for time course analysis with maSigPro
GLAD maSigPro GLAD maSigPro
updated 13.9 years ago by ★ 13k • written 13.9 years ago by ▴ 10
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4
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1.1k
views
Discrepancy on results from gcrma function and justGCRMA
gcrma GLAD gcrma GLAD
updated 14.3 years ago by 65k • written 14.3 years ago by ★ 2.0k
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4
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1.5k
views
Positive correlation between dye-swap technical replicates
Normalization Clustering probe limma GLAD Normalization Clustering probe limma GLAD
14.3 years ago Michał Góralski ▴ 40
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13
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1.7k
views
problem with data processing in R
PROcess GLAD PROcess GLAD
updated 14.4 years ago by ★ 1.7k • written 14.4 years ago by ▴ 170
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7
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1.4k
views
problem to compute copy number with crlmm
GLAD crlmm GLAD crlmm
updated 14.5 years ago by ▴ 250 • written 14.5 years ago by ▴ 40
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0
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1.0k
views
general CGH threshold question
aCGH CGH aCGH GLAD snapCGH aCGH CGH aCGH GLAD snapCGH
14.7 years ago Wolfgang RAFFELSBERGER ▴ 140
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0
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5.1k
views
Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
14.7 years ago Michael Dondrup ▴ 140
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4
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3.1k
views
retrieving mRNA sequences via biomaRt
GLAD biomaRt GLAD biomaRt
updated 14.8 years ago by ★ 13k • written 14.8 years ago by ▴ 30
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1
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1.1k
views
Normalized data in expresso and Expression Console differ
Normalization GLAD Normalization GLAD
updated 14.9 years ago by ★ 3.9k • written 14.9 years ago by ▴ 10
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0
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1.1k
views
browseGenome width question (rtracklayer)
Epigenetics GO hgu95av2 GLAD rtracklayer Epigenetics GO hgu95av2 GLAD rtracklayer
15.3 years ago Michael Lawrence ▴ 620
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0
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1.7k
views
getSeq human genomic sequences
Annotation Cancer BSgenome PROcess GLAD BSgenome IRanges Annotation Cancer BSgenome GLAD
15.3 years ago Hervé Pagès 16k
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2
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1.3k
views
Problem with Annotation of Mouse4302.db in simpleaffy
Annotation mouse4302 simpleaffy GLAD Annotation mouse4302 simpleaffy GLAD
updated 15.3 years ago by 65k • written 15.3 years ago by ▴ 40
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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