Showing : RNAseq • reset
1
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6
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2.6k
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edgeR - paired samples with multifactorial design - errors
RNASeq RNASeq
updated 11.5 years ago by ▴ 200 • written 11.5 years ago by ★ 13k
1
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12
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5.7k
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EdgeR: replicated pools, yes or not?
RNASeq Microarray edgeR RNASeq Microarray edgeR
updated 11.5 years ago by ★ 7.9k • written 11.5 years ago by ★ 13k
0
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1
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1.7k
views
Rsamtools - summarizeOverlaps - count read on complementary strand
RNASeq RNASeq
updated 11.5 years ago by ▴ 200 • written 11.5 years ago by ★ 13k
0
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0
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4.2k
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Interpretation of fold.changes for covariates in a linear model using voom
RNASeq RNASeq
11.5 years ago Gordon Smyth 53k
0
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0
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4.5k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
11.5 years ago Dan Tenenbaum ★ 8.2k
0
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0
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1.1k
views
Interpretation of fold.changes for covariates in a linear model using voom
RNASeq RNASeq
11.5 years ago Guest User ★ 13k
0
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0
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1.7k
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easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
11.5 years ago Guest User ★ 13k
3
votes
4
replies
4.9k
views
What is the easiest way to make the GC content and length matrix for package cqn?
RNASeq edgeR cqn RNASeq edgeR cqn
updated 11.5 years ago by 25k • written 11.5 years ago by ▴ 380
0
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0
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741
views
Join expression values of replicas in edgeR
Sequencing RNASeq edgeR Sequencing RNASeq edgeR
11.5 years ago Gordon Smyth 53k
0
votes
1
reply
1.3k
views
countOverlaps gives an empty SummarizeExperiments
RNASeq Alignment biomaRt rtracklayer DESeq RNASeq Alignment biomaRt rtracklayer DESeq
updated 11.6 years ago by 25k • written 11.6 years ago by ★ 13k
0
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0
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683
views
Join expression values of replicas in edgeR
RNASeq edgeR RNASeq edgeR
11.6 years ago María Jesús García ▴ 30
1
vote
3
replies
2.7k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 11.6 years ago by 16k • written 11.6 years ago by ★ 11k
0
votes
2
replies
2.7k
views
creating contrast matrix (limma) for two factorial in R
RNASeq limma RNASeq limma
updated 11.6 years ago by ★ 7.9k • written 11.6 years ago by ▴ 20
0
votes
1
reply
2.2k
views
edgeR time series analysis question
RNASeq RNASeq
updated 11.6 years ago by 53k • written 11.6 years ago by ★ 13k
0
votes
1
reply
5.6k
views
DESeq2 comparison of treatment in two conditions
RNASeq RNASeq
updated 11.6 years ago by 43k • written 11.6 years ago by ▴ 140
0
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3
replies
2.5k
views
Questiond about the descrepancy between edgeR and limma-voom
RNASeq edgeR RNASeq edgeR
updated 11.6 years ago by ▴ 380 • written 11.6 years ago by ▴ 900
0
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0
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1.3k
views
Questiond about the descrepancy between edgeR and limma-voom
RNASeq edgeR RNASeq edgeR
11.6 years ago Ming ▴ 380
0
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0
replies
2.7k
views
WGCNA RNAseq
RNASeq Cancer trigger RNASeq Cancer trigger
11.6 years ago Anna Esteve Codina ▴ 20
0
votes
5
replies
2.2k
views
How does pathview deal with enzyme with several coding genes?
RNASeq Organism pathview RNASeq Organism pathview
11.7 years ago 刘鹏飞 ▴ 80
0
votes
0
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1.7k
views
goseq: pwf: Error in if (hi <= low) { : missing value where TRUE/FALSE needed
RNASeq GO goseq DESeq2 RNASeq GO goseq DESeq2
11.7 years ago 刘鹏飞 ▴ 80
0
votes
6
replies
5.4k
views
DESeq2 - input data questions
RNASeq edgeR DESeq DESeq2 RNASeq edgeR DESeq DESeq2
updated 11.7 years ago by 43k • written 11.7 years ago by ▴ 380
0
votes
1
reply
2.1k
views
edgeR, multifactorial design
RNASeq Cancer edgeR RNASeq Cancer edgeR
updated 11.7 years ago by 53k • written 11.7 years ago by ▴ 70
1
vote
3
replies
2.0k
views
questions on edgeR package
RNASeq edgeR Rsubread RNASeq edgeR Rsubread
updated 11.7 years ago by ▴ 100 • written 11.7 years ago by 53k
1
vote
5
replies
5.1k
views
limma-voom
RNASeq Normalization limma edgeR RNASeq Normalization limma edgeR
updated 3.6 years ago by 53k • written 11.7 years ago by ▴ 380
0
votes
0
replies
1.2k
views
Seattle Short Course, Feb 27-28: Introduction to Bioconductor for Sequence Analysis
RNASeq Visualization Cancer RNASeq Visualization Cancer
11.7 years ago Martin Morgan 25k
0
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0
replies
1.6k
views
ChIPpeakAnno: 6-way venn diagram
RNASeq ChIPpeakAnno RNASeq ChIPpeakAnno
11.7 years ago Julie Zhu ★ 4.3k
0
votes
4
replies
1.6k
views
finding a very large number of false positives using edgeR
Sequencing RNASeq edgeR Sequencing RNASeq edgeR
updated 11.8 years ago by 53k • written 11.8 years ago by ▴ 20
0
votes
4
replies
1.9k
views
AllelicImbalance with VCFs?
RNASeq Cancer trio AllelicImbalance RNASeq Cancer trio AllelicImbalance
updated 11.8 years ago by ▴ 20 • written 11.8 years ago by ▴ 10
0
votes
0
replies
1.3k
views
An introductory course to RNA-seq at MBC Via Nizza 52, Torino, Italy, 25-27 March 2014
RNASeq RNASeq
11.8 years ago raffaele calogero ▴ 500
0
votes
1
reply
990
views
EdgeR multi-factor testing questions
RNASeq edgeR RNASeq edgeR
updated 11.8 years ago by 53k • written 11.8 years ago by ★ 13k
0
votes
1
reply
1.3k
views
calcNormFactors gives me NaN
RNASeq edgeR a4 RNASeq edgeR a4
updated 11.8 years ago by ★ 7.9k • written 11.8 years ago by ★ 13k
0
votes
2
replies
1.8k
views
easyRNAseq and DEseq for no replicate RNAseq
RNASeq PROcess easyRNASeq RNASeq PROcess easyRNASeq
updated 11.9 years ago by ▴ 320 • written 11.9 years ago by ▴ 10
0
votes
1
reply
672
views
RNAseq visualization tools
RNASeq RNASeq
updated 11.9 years ago by ★ 7.9k • written 11.9 years ago by ▴ 30
0
votes
5
replies
2.2k
views
SCAN.UPC for Illumina arrays?
RNASeq qPCR affy oligo frma RNASeq qPCR affy oligo frma
updated 11.9 years ago by ▴ 600 • written 11.9 years ago by ★ 4.2k
0
votes
1
reply
1.4k
views
Random effect for RNAseq data in Limma package
RNASeq Microarray limma RNASeq Microarray limma
updated 11.9 years ago by 53k • written 11.9 years ago by ▴ 10
0
votes
1
reply
1.8k
views
help: goseq and makeOrgPackageFromNCBI in AnnotationForge
RNASeq GO Organism AnnotationDbi goseq RNASeq GO Organism AnnotationDbi goseq
updated 11.9 years ago by ★ 7.2k • written 12.0 years ago by ▴ 80
0
votes
8
replies
2.4k
views
Dexseq package: dexseq_count error message and warnings
RNASeq RNASeq
updated 11.9 years ago by ★ 1.9k • written 12.0 years ago by ▴ 230
0
votes
10
replies
3.3k
views
ANCOVA microarray time-course continuous & categorical variables / Limma extensions
RNASeq Microarray limma RNASeq Microarray limma
updated 12.0 years ago by 53k • written 12.0 years ago by ▴ 380
0
votes
0
replies
903
views
RNAseq in silico simulator
RNASeq Biostrings RNASeq Biostrings
12.0 years ago Dave Gerrard ▴ 40
0
votes
5
replies
2.1k
views
EasyRNAseq - error in building count table - Error in unlist
Sequencing RNASeq edgeR easyRNASeq Sequencing RNASeq edgeR easyRNASeq
updated 12.1 years ago by ★ 1.2k • written 12.1 years ago by ★ 13k
0
votes
0
replies
2.6k
views
8. CGHCall problems (Bernard North [guest]) : Bioconductor Digest, Vol 126, Issue 7
aCGH RNASeq ChIPSeq Proteomics Annotation Normalization GO Network Cancer ChipName probe
12.1 years ago Sarah JugurnauthLittle ▴ 20
0
votes
2
replies
6.0k
views
sva + voom + limma
RNASeq Microarray sva RNASeq Microarray sva
updated 12.1 years ago by 53k • written 12.1 years ago by ▴ 120
0
votes
1
reply
1.1k
views
TCC RNAseq normalization package error
RNASeq TCC RNASeq TCC
updated 12.2 years ago by ★ 7.9k • written 12.2 years ago by ★ 13k
0
votes
6
replies
1.9k
views
request
RNASeq DESeq RNASeq DESeq
12.2 years ago Alexey Moskalev ▴ 30
0
votes
2
replies
5.0k
views
Bioconductor: CPM and log(CPM) values in EdgeR does not match
RNASeq edgeR RNASeq edgeR
updated 12.2 years ago by ▴ 350 • written 12.2 years ago by ▴ 10
0
votes
6
replies
3.8k
views
RNASeq:- getting Zero Count
RNASeq RNASeq
updated 12.2 years ago by ★ 6.8k • written 12.2 years ago by ▴ 570
0
votes
2
replies
1.2k
views
RNAseq data normalization without differential expression
RNASeq Normalization edgeR DESeq RNASeq Normalization edgeR DESeq
updated 12.2 years ago by 43k • written 12.2 years ago by ▴ 180
0
votes
4
replies
2.2k
views
DexSeq extracols option
RNASeq Microarray Genetics Annotation Normalization Infrastructure Cancer probe limma
updated 12.2 years ago by ★ 1.9k • written 12.2 years ago by ▴ 40
0
votes
0
replies
1.3k
views
Question about quality of biological replicates from RNAseq data
RNASeq edgeR RNASeq edgeR
12.2 years ago sheng zhao ▴ 90
0
votes
0
replies
1.2k
views
Question about quality of biological replicates when using edgeR
RNASeq edgeR RNASeq edgeR
12.2 years ago sheng zhao ▴ 90
1,409 results • Page 26 of 29
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Replies
Comment: Memory error while running alignments by Erik Wright ▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Comment: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by Gabriel • 0
Thank you very much for the reply. However, none of these three options seems to fit: 1) The genes for which NA appears do not have all 0 …
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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