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
10.9 years ago Rory Stark ★ 5.2k
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1.1k
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Limma design : What is the
GLAD GLAD
11.0 years ago Santy Marques-Ladeira ▴ 20
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3
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1.5k
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GLAD crashes when built with gcc-4.8
GLAD GLAD
updated 11.1 years ago by 25k • written 11.1 years ago by ▴ 70
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876
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arrayQualityMetrics does not produce interactive plots
GLAD GLAD
11.1 years ago Wolfgang Huber ★ 13k
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makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
11.4 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
11.5 years ago Rory Stark ★ 5.2k
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1
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1.2k
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beadarray library: perBeadFile
GLAD beadarray GLAD beadarray
updated 11.5 years ago by ★ 6.6k • written 11.5 years ago by ▴ 10
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1
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1.9k
views
Issue of installing the GLAD package
GLAD GLAD
updated 11.7 years ago by 1.6k • written 11.7 years ago by ★ 13k
1
vote
1
reply
2.3k
views
multiple threads on QuasR
Alignment GLAD QuasR Alignment GLAD QuasR
11.8 years ago Michael Stadler ▴ 350
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1.1k
views
rhdf5 and factors
GO GLAD GO GLAD
12.0 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 12.2 years ago by ★ 1.3k • written 12.2 years ago by ▴ 160
0
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979
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question on easyRNASeq developer version
GLAD easyRNASeq GLAD easyRNASeq
12.3 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 12.4 years ago by ★ 13k • written 12.4 years ago by ▴ 20
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1.3k
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question regarding ChIPPeakAnno use
Annotation annotate GLAD ChIPpeakAnno Annotation annotate GLAD ChIPpeakAnno
12.4 years ago Julie Zhu ★ 4.3k
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HTqPCR problems
Microarray qPCR GO Preprocessing GLAD HTqPCR Microarray qPCR GO Preprocessing GLAD
12.4 years ago cfischer ▴ 10
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926
views
(no subject)
Clustering probe limma GLAD Clustering probe limma GLAD
12.5 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 12.6 years ago by ▴ 340 • written 12.6 years ago by ★ 2.0k
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votes
6
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2.5k
views
HTqPCR
qPCR GO GLAD HTqPCR qPCR GO GLAD HTqPCR
updated 12.6 years ago by ★ 2.0k • written 12.6 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 12.7 years ago by 16k • written 12.7 years ago by ▴ 740
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2.8k
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gene set enrichment analysis of RNA-Seq data
Microarray limma GLAD edgeR goseq Microarray limma GLAD edgeR goseq
12.7 years ago Paolo Guarnieri ▴ 20
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1.3k
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Fwd: RCytoscape couldn't connect to host
GO GLAD RCytoscape GO GLAD RCytoscape
12.8 years ago Paul Shannon ▴ 750
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1.4k
views
[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
13.0 years ago Valerie Obenchain ★ 6.8k
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1
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1.8k
views
Rgraphviz installing problem
Rgraphviz GLAD Rgraphviz GLAD
updated 13.0 years ago by 25k • written 13.0 years ago by ▴ 10
0
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1
reply
986
views
[Rocky] - LIMMA to identify deferentially expressed genes
affy limma GLAD affy limma GLAD
updated 13.0 years ago by 21k • written 13.0 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
13.2 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 13.2 years ago by 25k • written 13.2 years ago by ▴ 110
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1
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1.8k
views
[Bioc-sig-seq] as.data.frame on GRanges object with DNAStringSet in values
Cancer Biostrings GLAD Cancer Biostrings GLAD
updated 13.3 years ago by ★ 11k • written 13.3 years ago by 16k
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1.7k
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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
13.4 years ago Lavorgna Giovanni ▴ 80
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2
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977
views
Help with the weaver example from limma package
Annotation GLAD Annotation GLAD
updated 13.6 years ago by 52k • written 13.6 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 13.8 years ago by 25k • written 13.8 years ago by ▴ 10
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1
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1.5k
views
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 13.8 years ago by ▴ 100 • written 13.8 years ago by 52k
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1
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1.5k
views
edgeR glm fit error
GO GLAD edgeR GO GLAD edgeR
13.9 years ago Gordon Smyth 52k
0
votes
1
reply
961
views
Newbie question
GLAD GLAD
updated 14.0 years ago by 67k • written 14.0 years ago by ▴ 30
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1
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1.6k
views
[Rocky] - Clarification for finding SNPs at 3'UTR, 5'UTR, CDS genomic regions
SNP Cancer GLAD SNP Cancer GLAD
updated 14.1 years ago by 16k • written 14.1 years ago by ▴ 30
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2
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2.4k
views
problem installing 'GLAD' package
cdf GLAD cdf GLAD
14.2 years ago Shenglin Zheng ▴ 20
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989
views
HTqPCR question
Microarray limma GLAD HTqPCR Microarray limma GLAD HTqPCR
14.2 years ago Heidi Dvinge ★ 2.0k
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1.3k
views
error in plotKEGGGraph
Pathways GLAD KEGGgraph Pathways GLAD KEGGgraph
14.3 years ago Robert M. Flight ▴ 280
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1
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1.5k
views
write.XStringView/write.XStringSet highly inefficient (solved)
Cancer BSgenome PROcess GLAD BSgenome Cancer BSgenome PROcess GLAD BSgenome
updated 14.5 years ago by ★ 13k • written 14.5 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 14.7 years ago by ★ 13k • written 14.7 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 15.0 years ago by 67k • written 15.0 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
15.1 years ago • updated 15.0 years ago Michał Góralski ▴ 40
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13
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2.1k
views
problem with data processing in R
PROcess GLAD PROcess GLAD
updated 15.1 years ago by ★ 1.7k • written 15.2 years ago by ▴ 170
0
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7
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1.7k
views
problem to compute copy number with crlmm
GLAD crlmm GLAD crlmm
updated 15.2 years ago by ▴ 250 • written 15.2 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
15.5 years ago Wolfgang RAFFELSBERGER ▴ 140
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0
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5.5k
views
Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
15.5 years ago Michael Dondrup ▴ 140
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4
replies
3.5k
views
retrieving mRNA sequences via biomaRt
GLAD biomaRt GLAD biomaRt
updated 15.5 years ago by ★ 13k • written 15.5 years ago by ▴ 30
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votes
1
reply
1.3k
views
Normalized data in expresso and Expression Console differ
Normalization GLAD Normalization GLAD
updated 15.6 years ago by ★ 3.9k • written 15.6 years ago by ▴ 10
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0
replies
1.2k
views
browseGenome width question (rtracklayer)
Epigenetics GO hgu95av2 GLAD rtracklayer Epigenetics GO hgu95av2 GLAD rtracklayer
16.0 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
16.0 years ago Hervé Pagès 16k
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votes
2
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1.5k
views
Problem with Annotation of Mouse4302.db in simpleaffy
Annotation mouse4302 simpleaffy GLAD Annotation mouse4302 simpleaffy GLAD
updated 16.0 years ago by 67k • written 16.0 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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