Showing : PROcess • reset
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Pathview+GAGE workflow on RNA-seq data pathway analysis and visualization (was: Pathview published in Bioinformatics)
Annotation Pathways Visualization graph PROcess gage pathview Annotation Pathways graph
12.5 years ago Luo Weijun ★ 1.6k
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Suggestion - gene set enrichment of genes against BP and Disease gene sets
Microarray PROcess Microarray PROcess
12.5 years ago Bade ▴ 310
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4
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7.3k
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Too many (?) differentially expressed genes - edgeR and DESeq
PROcess edgeR DESeq PROcess edgeR DESeq
updated 12.5 years ago by ★ 13k • written 12.5 years ago by ▴ 130
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3
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1.7k
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Normalize background on marray Agilent object
Normalization limma PROcess marray Normalization limma PROcess marray
updated 12.5 years ago by 53k • written 12.6 years ago by ▴ 50
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1.3k
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DEXSeq Help Needed: newExonCountSet() error messages
PROcess DEXSeq PROcess DEXSeq
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 150
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info on pathview
graph PROcess pathview graph PROcess pathview
12.6 years ago Luo Weijun ★ 1.6k
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1.4k
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edgeR: very low p-value and very high variance within the group of replicates
limma PROcess edgeR limma PROcess edgeR
12.6 years ago Gordon Smyth 53k
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1.2k
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goseq and transcript length
Annotation GO PROcess goseq Annotation GO PROcess goseq
12.6 years ago Xulong Wang ▴ 10
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1
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2.1k
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goseq and transcript length data
Annotation GO PROcess goseq Annotation GO PROcess goseq
updated 12.6 years ago by ▴ 320 • written 12.7 years ago by ★ 13k
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9
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2.7k
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beadarray - combining swath files
PROcess beadarray PROcess beadarray
updated 12.7 years ago by ★ 1.1k • written 12.7 years ago by ▴ 70
0
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using beadarray to process iscan expression data - error using readIllumina()
PROcess beadarray PROcess beadarray
12.7 years ago Darren Plant ▴ 70
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3
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2.9k
views
DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 12.7 years ago by 43k • written 12.7 years ago by ▴ 150
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1
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2.1k
views
DEXSeq Problems
Alignment Homo sapiens PROcess Alignment Homo sapiens PROcess
updated 12.7 years ago by ★ 3.8k • written 12.7 years ago by ▴ 150
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1.6k
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How do I background correct an Illumina eset without using lumiB
Microarray probe limma PROcess convert beadarray lumi Microarray probe limma PROcess
12.7 years ago Gordon Smyth 53k
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1
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1.7k
views
How do I background correct an Illumina eset without using lumiB?
Microarray probe PROcess convert beadarray lumi Microarray probe PROcess convert lumi
updated 12.7 years ago by ▴ 440 • written 12.7 years ago by ★ 13k
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7
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4.1k
views
VariantAnnotation: Performance and memory issues in readVcf
VariantAnnotation PROcess Rsamtools VariantAnnotation VariantAnnotation PROcess Rsamtools
updated 12.7 years ago by 6.7k • written 12.7 years ago by ▴ 300
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1
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1.9k
views
SCAN-UPC: 12079 of 22283 probes returned for hgu133a CELs?
Normalization hgu133a probe affy PROcess SCAN.UPC Normalization hgu133a probe affy
updated 12.7 years ago by ▴ 20 • written 12.7 years ago by ▴ 600
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3
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1.5k
views
Deleting object rows while looping - II
Coverage Alignment Cancer PROcess Coverage Alignment Cancer PROcess
updated 12.7 years ago by ★ 13k • written 12.7 years ago by 16k
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3
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1.9k
views
Deleting object rows while looping - II
Coverage Alignment PROcess Coverage Alignment PROcess
updated 12.8 years ago by 25k • written 12.8 years ago by ▴ 90
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1.3k
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RNAseq analyses: to use, or not use, all the samples; that's the question.
PROcess edgeR DESeq PROcess edgeR DESeq
12.8 years ago Aaron Mackey ▴ 200
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5
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2.5k
views
Question regarding cellhts2 output
Normalization Visualization PROcess cellHTS2 ASSIGN Normalization Visualization PROcess
12.8 years ago maziz@tgen.org ▴ 70
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2
replies
1.7k
views
BitSeq transcript IDs
Alignment PROcess BitSeq Alignment PROcess BitSeq
updated 12.8 years ago by ▴ 30 • written 12.8 years ago by ▴ 70
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6
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1.7k
views
definition for intergenic SNPs in locateVariants function
PROcess PROcess
12.8 years ago Adaikalavan Ramasamy ▴ 220
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1
reply
1.4k
views
BitSeq getExpression crash
Alignment PROcess BitSeq Alignment PROcess BitSeq
updated 12.8 years ago by ▴ 70 • written 12.8 years ago by ▴ 30
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1.5k
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MCS & ChemineR
Network Clustering PROcess ChemmineR Network Clustering PROcess ChemmineR
12.9 years ago Thomas Girke ★ 1.7k
0
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5
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2.7k
views
yieldSize and paired end data in SummarizeOverlaps error?
BSgenome PROcess BSgenome ASSIGN BSgenome PROcess BSgenome ASSIGN
updated 12.9 years ago by ★ 6.8k • written 12.9 years ago by ▴ 10
3
votes
3
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2.0k
views
EBImage: filtering in the presence of NAs
PROcess EBImage PROcess EBImage
updated 12.9 years ago by ★ 13k • written 12.9 years ago by ▴ 60
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4
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1.0k
views
biocLite and unknown svn revision
PROcess PROcess
updated 12.9 years ago by 25k • written 12.9 years ago by ★ 11k
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17
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9.6k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
Annotation Normalization GO PROcess oligo Annotation Normalization GO PROcess oligo
updated 12.9 years ago by 68k • written 12.9 years ago by ▴ 100
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2.1k
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AgiMicroRna for new Agilent Chip format
Microarray GO limma PROcess microRNA AgiMicroRna Microarray GO limma PROcess microRNA
12.9 years ago Gordon Smyth 53k
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1
reply
1.1k
views
Difference between number of probes and number of data rows using 'oligo' on Affy miRNA v3.0 arrays
probe PROcess probe PROcess
updated 12.9 years ago by 68k • written 12.9 years ago by ▴ 10
0
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1.7k
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How can I use the information from an ADF [Array Design File] file for microarray normalization?
Normalization cdf PROcess convert Normalization cdf PROcess convert
12.9 years ago Christoph Geisenberger ▴ 10
0
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3
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2.5k
views
runSPIA() in graphite package
Pathways Breast siggenes PROcess cycle graphite Pathways Breast siggenes PROcess cycle
updated 13.0 years ago by ▴ 20 • written 13.0 years ago by ▴ 420
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1
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2.2k
views
limma-voom and y$E
Normalization limma PROcess Normalization limma PROcess
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 240
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1.6k
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how to supply a vector/list of results to GenTable in topGO?
GO PROcess topGO GO PROcess topGO
13.0 years ago Adrian Alexa ▴ 400
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1.5k
views
FlowCore - reading in flowSets
FlowCytometry PROcess flowCore FlowCytometry PROcess flowCore
13.0 years ago Pieter Coussement ▴ 30
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3.0k
views
normalization of illumina bead array data
PROcess PROcess
updated 13.0 years ago by ▴ 90 • written 13.1 years ago by ★ 3.6k
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5
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3.4k
views
parallel and GSVA
PROcess GSVA PROcess GSVA
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 130
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1.0k
views
detailed analysis process of Comparisons Both Between and Within Subjects of edgeR
PROcess edgeR PROcess edgeR
13.1 years ago Gordon Smyth 53k
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4
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3.0k
views
minfi - how to subset a GenomicMethylSet by chromosome/seqname
Microarray Annotation PROcess minfi Microarray Annotation PROcess minfi
updated 13.1 years ago by ★ 4.2k • written 13.1 years ago by ▴ 30
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1
reply
1.1k
views
IMA Peak Correction Error - subscript out of bounds
Annotation PROcess Annotation PROcess
updated 13.1 years ago by ★ 8.2k • written 13.1 years ago by ★ 13k
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0
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795
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detailed analysis process of "Comparisons Both Between and Within Subjects" of edgeR
PROcess edgeR PROcess edgeR
13.1 years ago Huajing Teng ▴ 20
0
votes
1
reply
1.4k
views
normalization of illumina bead array data
PROcess PROcess
13.1 years ago Michele ▴ 90
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0
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1.2k
views
[Bioconductor] normalization of illumina bead array data
PROcess PROcess
13.1 years ago Michele ▴ 90
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votes
5
replies
2.1k
views
oligo package
Microarray Annotation annotate PROcess Microarray Annotation annotate PROcess
updated 13.1 years ago by 68k • written 13.1 years ago by ★ 13k
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1
reply
1.8k
views
edgeR:Differences in results between two different versions of edgeR
PROcess edgeR PROcess edgeR
updated 13.2 years ago by 53k • written 13.2 years ago by ▴ 60
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votes
7
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4.5k
views
Weird things happening with minfi and RcppEigen
PROcess minfi PROcess minfi
updated 13.2 years ago by ★ 4.3k • written 13.2 years ago by ▴ 440
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votes
3
replies
3.5k
views
Subsetting expression sets for mass spec data - second ask
Classification Cancer PROcess Classification Cancer PROcess
updated 13.2 years ago by 21k • written 13.2 years ago by ▴ 300
0
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0
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1.5k
views
Using aCGH library on Affymetrix Cytogenetics 2.7M microarray data
aCGH SNP PROcess aCGH aCGH SNP PROcess aCGH
13.2 years ago Guest User ★ 13k
0
votes
2
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1.9k
views
frma for Nimblegen arrays?
Microarray Annotation Normalization affy PROcess safe frma frmaTools Microarray affy
updated 13.2 years ago by ★ 4.3k • written 13.2 years ago by ▴ 260
651 results • Page 3 of 14
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Comment: Bile acid analysis with limpa by ATpoint ★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help by Jeremy • 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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