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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912
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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 10.3 years ago by 25k • written 10.3 years ago by ▴ 70
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766
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arrayQualityMetrics does not produce interactive plots
GLAD GLAD
10.4 years ago Wolfgang Huber ★ 13k
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2.2k
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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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1.9k
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
views
beadarray library: perBeadFile
GLAD beadarray GLAD beadarray
updated 10.7 years ago by ★ 6.5k • written 10.7 years ago by ▴ 10
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1
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1.7k
views
Issue of installing the GLAD package
GLAD GLAD
updated 10.9 years ago by 1.6k • written 10.9 years ago by ★ 13k
1
vote
1
reply
2.0k
views
multiple threads on QuasR
Alignment GLAD QuasR Alignment GLAD QuasR
11.0 years ago Michael Stadler ▴ 350
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923
views
rhdf5 and factors
GO GLAD GO GLAD
11.2 years ago Stephen Eglen ▴ 10
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3
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1.6k
views
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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0
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854
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question on easyRNASeq developer version
GLAD easyRNASeq GLAD easyRNASeq
11.5 years ago delhomme@embl.de ★ 1.2k
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2
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1.5k
views
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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0
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1.1k
views
question regarding ChIPPeakAnno use
Annotation annotate GLAD ChIPpeakAnno Annotation annotate GLAD ChIPpeakAnno
11.6 years ago Julie Zhu ★ 4.3k
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1.1k
views
HTqPCR problems
Microarray qPCR GO Preprocessing GLAD HTqPCR Microarray qPCR GO Preprocessing GLAD
11.7 years ago cfischer ▴ 10
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0
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813
views
(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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votes
6
replies
2.2k
views
HTqPCR
qPCR GO GLAD HTqPCR qPCR GO GLAD HTqPCR
updated 11.8 years ago by ★ 2.0k • written 11.9 years ago by ▴ 40
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13
replies
1.9k
views
PWMscoreStartingAt and ambiguous subject seqs
Cancer Biostrings GLAD Cancer Biostrings GLAD
updated 11.9 years ago by 16k • written 11.9 years ago by ▴ 740
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0
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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
views
Fwd: RCytoscape couldn't connect to host
GO GLAD RCytoscape GO GLAD RCytoscape
12.0 years ago Paul Shannon ▴ 750
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0
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1.2k
views
[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
12.2 years ago Valerie Obenchain ★ 6.8k
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1
reply
1.6k
views
Rgraphviz installing problem
Rgraphviz GLAD Rgraphviz GLAD
updated 12.3 years ago by 25k • written 12.3 years ago by ▴ 10
0
votes
1
reply
865
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
views
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
reply
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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0
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1.5k
views
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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839
views
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
reply
878
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
0
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1
reply
1.3k
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 13.0 years ago by ▴ 100 • written 13.0 years ago by 50k
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1
reply
1.3k
views
edgeR glm fit error
GO GLAD edgeR GO GLAD edgeR
13.2 years ago Gordon Smyth 50k
0
votes
1
reply
844
views
Newbie question
GLAD GLAD
updated 13.3 years ago by 65k • written 13.3 years ago by ▴ 30
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1
reply
1.4k
views
[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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0
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874
views
HTqPCR question
Microarray limma GLAD HTqPCR Microarray limma GLAD HTqPCR
13.4 years ago Heidi Dvinge ★ 2.0k
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0
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1.1k
views
error in plotKEGGGraph
Pathways GLAD KEGGgraph Pathways GLAD KEGGgraph
13.6 years ago Robert M. Flight ▴ 280
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1
reply
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
reply
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 14.2 years ago by 65k • written 14.2 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
0
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7
replies
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
0
votes
0
replies
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
replies
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
replies
3.1k
views
retrieving mRNA sequences via biomaRt
GLAD biomaRt GLAD biomaRt
updated 14.7 years ago by ★ 13k • written 14.7 years ago by ▴ 30
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1
reply
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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votes
0
replies
1.1k
views
browseGenome width question (rtracklayer)
Epigenetics GO hgu95av2 GLAD rtracklayer Epigenetics GO hgu95av2 GLAD rtracklayer
15.2 years ago Michael Lawrence ▴ 620
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votes
0
replies
1.7k
views
getSeq human genomic sequences
Annotation Cancer BSgenome PROcess GLAD BSgenome IRanges Annotation Cancer BSgenome GLAD
15.2 years ago Hervé Pagès 16k
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votes
2
replies
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
Recent ...
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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