Showing : glad • reset
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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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1.1k
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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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1
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1.1k
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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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1.2k
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error in plotKEGGGraph
Pathways GLAD KEGGgraph Pathways GLAD KEGGgraph
13.6 years ago Robert M. Flight ▴ 280
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0
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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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0
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1.1k
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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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3
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2.0k
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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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982
views
Re: Bioconductor digest, Vol 1 #134 - 5 msgs
cdf multtest affy GLAD cdf multtest affy GLAD
updated 21.6 years ago by ★ 2.3k • written 21.6 years ago by ▴ 10
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2
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881
views
Re: Better mailing list archives {was "Searching BioC .."}
GLAD GLAD
20.6 years ago Warnes, Gregory R ▴ 460
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0
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947
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affy, how to define the normalization method that works with my data
Normalization affy GLAD Normalization affy GLAD
19.8 years ago Dipl.-Ing. Johannes Rainer ▴ 430
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votes
1
reply
600
views
questions about limma
Microarray limma GLAD Microarray limma GLAD
updated 19.7 years ago by 65k • written 19.7 years ago by ▴ 10
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0
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610
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GeneExpressionOmnibus (GEO) question
AnnBuilder GLAD AnnBuilder GLAD
19.5 years ago Ilya Venger ▴ 20
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0
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1.3k
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Metrology for Gene Expression -- Postdoc Opportunities at NIST
Microarray PROcess GLAD attract Microarray PROcess GLAD attract
19.4 years ago Marc Salit ▴ 80
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8
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1.5k
views
Gene Selection
GLAD GLAD
updated 19.2 years ago by ▴ 210 • written 19.3 years ago by ▴ 310
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0
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1.1k
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Detecting overrepresented genomic loci
aCGH Clustering CGH geneplotter DNAcopy aCGH GLAD aCGH Clustering CGH geneplotter aCGH
19.1 years ago Yi, Andrew ▴ 20
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1
reply
795
views
error message from GLAD
CGH GLAD CGH GLAD
updated 18.7 years ago by ▴ 20 • written 18.7 years ago by ▴ 30
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0
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657
views
Rosetta vs Limma
limma GLAD limma GLAD
18.5 years ago Gordon Smyth 50k
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0
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607
views
geneName in GEOquery package
affy GLAD GEOquery affy GLAD GEOquery
18.3 years ago Sean Davis 21k
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1.1k
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Analysing categorical CGH data
Clustering Cancer CGH GLAD made4 Clustering Cancer CGH GLAD made4
17.7 years ago Aedin Culhane ▴ 510
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649
views
fedora core 5 x86_64 rpm extras
GLAD GLAD
17.6 years ago D.Enrique ESCOBAR ESPINOZA ▴ 360
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1
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1.1k
views
Help with GenePix files
Normalization marray GLAD Normalization marray GLAD
updated 17.2 years ago by ★ 7.4k • written 17.2 years ago by ▴ 310
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955
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FDR of enrichment analysis and other questions on GOstats
Cancer GOstats GLAD Cancer GOstats GLAD
16.8 years ago Serge Eifes ▴ 90
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0
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784
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how to get fewer cut points with DNAcopy or GLAD
SNP affy DNAcopy GLAD SNP affy DNAcopy GLAD
16.7 years ago Wittner, Ben ▴ 290
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7
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1.8k
views
segmentation for Affy SNP arrays
SNP CGH affy GLAD snapCGH SNP CGH affy GLAD snapCGH
updated 16.6 years ago by ▴ 250 • written 16.6 years ago by ▴ 440
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2
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1.2k
views
Chromosome 23 and 24 dropped after run snapCGH processCGH
aCGH Survival Cancer annotate genefilter affy DNAcopy aCGH GLAD tilingArray snapCGH
updated 16.6 years ago by ▴ 40 • written 16.6 years ago by ▴ 110
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4
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1.4k
views
running time of snapCGH processCGH and runDNAcopy
aCGH Survival CGH annotate genefilter affy DNAcopy aCGH GLAD tilingArray snapCGH aCGH
updated 16.6 years ago by ▴ 230 • written 16.6 years ago by ▴ 110
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2
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1.1k
views
hyperGTest and HyperGParams
Microarray Annotation GLAD Category Microarray Annotation GLAD Category
updated 16.5 years ago by ★ 5.5k • written 16.5 years ago by ▴ 500
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1
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1.1k
views
Help needed with aroma.affymetrix package to extract copy-numbers
Normalization cdf GLAD Normalization cdf GLAD
updated 16.2 years ago by ★ 2.4k • written 16.2 years ago by ▴ 270
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1.5k
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Cutoff to use for IQR filtering in genefilter
genefilter affy limma GeneSpring affylmGUI GLAD SIM genefilter affy limma GeneSpring
15.9 years ago Mark Cowley ▴ 400
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0
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696
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REPRESENTATIVES NEEDED @ STEELBEL.BE
GLAD GLAD
15.8 years ago R.HIMPE ▴ 10
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2
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1.3k
views
Adding a text label to the classvec colour bar in heatplot
Clustering Cancer graph GLAD Clustering Cancer graph GLAD
updated 15.8 years ago by ▴ 460 • written 15.8 years ago by ★ 6.5k
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1
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907
views
limma background correction
limma GLAD limma GLAD
updated 15.7 years ago by 50k • written 15.7 years ago by ▴ 340
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4
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1.3k
views
Problem in reading JPEG files for CGH arrays
aCGH Genetics aCGH GLAD aCGH Genetics aCGH GLAD
updated 15.3 years ago by 21k • written 15.3 years ago by ▴ 360
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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
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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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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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0
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1.0k
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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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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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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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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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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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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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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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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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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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votes
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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votes
1
reply
1.3k
views
edgeR glm fit error
GO GLAD edgeR GO GLAD edgeR
13.2 years ago Gordon Smyth 50k
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votes
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 13.1 years ago by ▴ 100 • written 13.0 years ago by 50k
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1
reply
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
0
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2
replies
842
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
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!
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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
A: Print Differentially Expressed Exons From Dexseq Results
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