7
votes
1
reply
15k
views
ERROR: No residual degrees of freedom in linear model fits
Microarray
updated 14 months ago by • 0 • written 10.0 years ago by ▴ 40
12
votes
15
replies
15k
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WGCNA: Understanding module-trait correlations
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updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 40
2
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5
replies
15k
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DESeq2: Paired Test
DESeq DESeq2 DESeq DESeq2
10.1 years ago • updated 10.0 years ago Pankaj Agarwal ▴ 100
9
votes
21
replies
15k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub dplyr
updated 21 months ago by ▴ 10 • written 3.5 years ago by ▴ 40
4
votes
7
replies
15k
views
package ‘edgeR’ is not available (for R version 3.1.2)
edgeR packages
9.2 years ago Patrick Schorderet ▴ 20
0
votes
4
replies
15k
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hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R pheatmap xcms
updated 20 months ago by 65k • written 2.7 years ago by • 0
2
votes
4
replies
15k
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biomaRt has encountered an unexpected server error.
biomaRt
updated 23 months ago by • 0 • written 4.1 years ago by • 0
25
votes
7
replies
14k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 7.5 years ago by ★ 3.7k • written 7.5 years ago by ▴ 30
0
votes
2
replies
14k
views
Error: install Bioconductor packages using BiocManager
software error
updated 4.5 years ago by 3.9k • written 4.5 years ago by • 0
8
votes
17
replies
14k
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WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
WGCNA Sample Size Outliers
updated 8.7 years ago by • 0 • written 9.2 years ago by ▴ 150
21
votes
5
replies
14k
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using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 9.0 years ago by 50k • written 10.0 years ago by ▴ 190
5
votes
14
replies
14k
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How to load GEO series matrix file in R Bioconductor
geoquery
updated 8.8 years ago by 21k • written 8.8 years ago by ▴ 10
3
votes
6
replies
14k
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Error: Faceting variables must have at least one value when plotting with ChIPQC
ChipQC chipqc
updated 19 months ago by • 0 • written 7.7 years ago by ▴ 10
16
votes
5
replies
14k
views
Error: Bioconductor version '3.8' requires R version '3.5'
software error
updated 5.0 years ago by ★ 6.5k • written 5.0 years ago by ▴ 10
3
votes
17
replies
14k
views
DESeq2 installation error
installation
updated 6.6 years ago by ▴ 100 • written 8.7 years ago by • 0
3
votes
11
replies
14k
views
Problems updating Bioconductor with R 3.2.0
upgrade r update
updated 9.0 years ago by ★ 8.2k • written 9.0 years ago by ▴ 10
34
votes
21
replies
14k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
9.6 years ago • updated 19 months ago Michael Love 41k
6
votes
1
reply
14k
views
Deseq2 PCA plot customize
deseq2 pca
updated 8.3 years ago by 41k • written 8.3 years ago by ▴ 40
0
votes
1
reply
14k
views
operations are possible only for numeric, logical or complex types
hgu133plus2 pathview hgu133plus2 pathview
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ★ 13k
3
votes
5
replies
14k
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cannot find -llapack + -lblas for package install
lblas llapack LinuxMint
9.0 years ago Eric P ▴ 10
6
votes
5
replies
14k
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Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 10
2
votes
13
replies
14k
views
Issues connecting with R 3.2.2 to source("http://bioconductor.org/biocLite.R")
spade
8.5 years ago frostbite907 • 0
14
votes
4
replies
14k
views
WGCNA Hub Gene Selection Method
WGCNA Hub Genes KmE Intramodular Connectivity
updated 8.8 years ago by ★ 3.0k • written 8.8 years ago by ▴ 150
0
votes
5
replies
14k
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cannot open file './', reason 'Permission denied' in: file(file, "r")
updated 16.7 years ago by ★ 13k • written 16.7 years ago by ▴ 50
18
votes
24
replies
14k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 3.2 years ago by • 0 • written 9.1 years ago by ▴ 120
0
votes
1
reply
14k
views
error under "hclust" for expression data
Clustering Clustering
updated 12.0 years ago by ▴ 610 • written 12.0 years ago by ▴ 180
5
votes
8
replies
14k
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Ensembl site unresponsive
ensembl biomart
updated 3.0 years ago by • 0 • written 3.6 years ago by ▴ 40
1
vote
13
replies
14k
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Count matrix from Kallisto as input for DESeq2
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7.7 years ago yjliu1127 • 0
6
votes
4
replies
14k
views
EdgeR Design matrix not of full rank
edger
updated 8.9 years ago by 50k • written 8.9 years ago by • 0
1
vote
13
replies
14k
views
GeneList issue ClusterProfiler
genelist clusterprofiler
6.9 years ago bhgyu ▴ 30
13
votes
20
replies
14k
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Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
EdgeR TCGA normalized count
updated 9.1 years ago by ▴ 130 • written 9.1 years ago by ▴ 10
4
votes
1
reply
14k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
5.7 years ago ansari.sarabio • 0
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 22 months ago by ▴ 30
11
votes
5
replies
13k
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Limma: how to get same output as topTable but for all the genes ?
limma toptable
updated 6.8 years ago by 50k • written 15.4 years ago by ▴ 190
2
votes
12
replies
13k
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Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
flowcore spillover
updated 6.4 years ago by ★ 1.3k • written 6.4 years ago by ▴ 20
0
votes
3
replies
13k
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Problem installing tximportData
tximportdata
7.1 years ago elg • 0
0
votes
9
replies
13k
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edgeR warnings and then error
edgeR edgeR
updated 11.5 years ago by 50k • written 11.5 years ago by ▴ 560
3
votes
1
reply
13k
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convert data in to expression set
limma convert limma convert
updated 10.9 years ago by ▴ 180 • written 10.9 years ago by ▴ 80
15
votes
9
replies
13k
views
Best way to convert uniprot accessions to entrez gene identifiers in R
org.hs.eg.db uniprot accessions entrez gene identifiers
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 160
2
votes
4
replies
13k
views
biomartRt: convert mouse gene symbol return multiple human gene symbol
biomart gene symbol
updated 8.8 years ago by ▴ 760 • written 9.0 years ago by ▴ 30
0
votes
4
replies
13k
views
Normalization by DEseq
Genetics Normalization DESeq Genetics Normalization DESeq
updated 6.2 years ago by • 0 • written 13.5 years ago by ▴ 20
17
votes
7
replies
13k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 10
0
votes
5
replies
13k
views
Error:The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as …
deseq2
updated 2.1 years ago by • 0 • written 3.6 years ago by • 0
3
votes
4
replies
13k
views
[GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?
updated 10.7 years ago by ★ 6.8k • written 10.7 years ago by ▴ 660
3
votes
4
replies
13k
views
converting ensembl transcript ID to ensemble gene: problem & missing values
biomart error ensembldb
6.2 years ago Yuqia • 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 28 days ago by • 0 • written 5.2 years ago by • 0
0
votes
1
reply
13k
views
Problem with installation of org.Hs.eg.db
software error org.hs.eg.db
updated 7.5 years ago by ★ 2.0k • written 7.5 years ago by • 0
0
votes
7
replies
13k
views
Applying DESeq on RSEM output
edgeR DESeq edgeR DESeq
updated 3.1 years ago by • 0 • written 11.1 years ago by ▴ 30
10
votes
4
replies
13k
views
Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
limma deseq2
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 30
5
votes
2
replies
13k
views
Complex Heatmap - hide one legend, show 2 - out off three annotations
complexheatmap bioconductor annotation heatmap legend
8.0 years ago • updated 7.9 years ago annkatrin.goepfert ▴ 10
45,610 results • Page 4 of 913
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Answer: DESeq2 v1.35.0 by Michael Love 41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by James W. MacDonald 65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0 by James W. MacDonald 65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by fatinataly • 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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