56
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8
replies
46k
views
conceptual question about FDR, FDR adjusted p-value and q-value
fdr qvalue
updated 5.6 years ago by 45k • written 9.4 years ago by ▴ 420
48
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20
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30k
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Batch correction in DESeq2
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updated 6.0 years ago by • 0 • written 6.4 years ago by ▴ 100
44
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29
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.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db pathview
updated 13 months ago by ▴ 130 • written 13 months ago by ▴ 160
40
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44
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Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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updated 4.4 years ago by ▴ 60 • written 5.0 years ago by ▴ 10
28
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43
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5.6k
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Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
findoverlaps granges
updated 6.1 years ago by 25k • written 6.2 years ago by ▴ 70
28
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25
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4.3k
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[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 4.8 years ago by ▴ 10 • written 5.3 years ago by ▴ 100
28
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19
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9.8k
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DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
7.7 years ago • updated 6 weeks ago Michael Love 37k
28
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16
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12k
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difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 4.1 years ago by ▴ 10 • written 5.9 years ago by ▴ 190
26
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8
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9.3k
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Removing continuous covariate effects in limma analysis
limma microarray
updated 4.7 years ago by 45k • written 7.1 years ago by ▴ 120
26
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16
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26k
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Differential expression analysis starting from TPM data
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updated 4.8 years ago by 45k • written 4.8 years ago by ▴ 60
25
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37
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7.5k
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Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq RSEM TCGA edgeR normalization
updated 5.4 years ago by 45k • written 5.4 years ago by ▴ 780
25
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9
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5.0k
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voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 7.3 years ago by 45k • written 7.3 years ago by ▴ 40
25
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11
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6.2k
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Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 6.5 years ago by ★ 3.7k • written 6.5 years ago by ▴ 70
25
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18
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Mapping genome regions to gene symbols
tcga cnv gene symbol coordinate
updated 7.1 years ago by ▴ 90 • written 7.1 years ago by ▴ 60
25
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0
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limma moderated t-statistics and B-statistics
Microarray limma
17.7 years ago • updated 19 months ago Gordon Smyth 45k
24
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7
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11k
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Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 5.6 years ago by ★ 3.7k • written 5.6 years ago by ▴ 30
24
votes
22
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13k
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DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 4.9 years ago by ▴ 100 • written 6.7 years ago by ▴ 190
23
votes
11
replies
858
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Bioconductor vs BioConductor
project
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 40
22
votes
10
replies
6.5k
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Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges chippeakanno
updated 5.2 years ago by ▴ 10 • written 5.2 years ago by ▴ 80
22
votes
4
replies
7.8k
views
Correct assumptions of using limma moderated t-test
limma statistical inference variance test bioconductor
updated 7.0 years ago by 45k • written 7.0 years ago by ▴ 780
22
votes
14
replies
31k
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deseq2 filter the low counts
deseq2 lowcount
updated 15 months ago by 37k • written 7.2 years ago by ▴ 30
21
votes
14
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1.2k
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biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 16 days ago by • 0 • written 5 weeks ago by ▴ 50
21
votes
10
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6.9k
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Tutorial: Bioconductor on Coursera
mooc Tutorial
updated 4.2 years ago by • 0 • written 6.7 years ago by 6.5k
21
votes
24
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10.0k
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Problem with biomart's listMarts function
biomart bug
updated 6.1 years ago by ▴ 470 • written 6.5 years ago by ★ 1.9k
21
votes
34
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5.0k
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Biomart error when updating to R 4.0.2
Biomart
updated 19 months ago by ★ 5.5k • written 19 months ago by ▴ 40
21
votes
12
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9.9k
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Nanostring analysis with limma
nanostring limma
updated 7.1 years ago by ▴ 20 • written 7.1 years ago by ▴ 350
20
votes
5
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using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 7.0 years ago by 45k • written 8.0 years ago by ▴ 180
20
votes
13
replies
20k
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gene dispersion, what does it mean?
gener rnaseq
updated 6.5 years ago by 45k • written 6.5 years ago by ▴ 60
20
votes
13
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2.2k
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News: markdown is coming to the support site
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4.8 years ago • updated 4.2 years ago Lucas Schiffer ▴ 240
20
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13
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Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger rnaseq
updated 7.6 years ago by 59k • written 7.6 years ago by ▴ 40
20
votes
12
replies
17k
views
New function lfcShrink() in DESeq2
deseq2
updated 2.8 years ago by • 0 • written 5.0 years ago by 37k
20
votes
7
replies
5.0k
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Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 4.6 years ago by 45k • written 4.6 years ago by • 0
19
votes
4
replies
6.2k
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Confidence intervals on edgeR logFC
edgeR statistics confidence interval
updated 6.1 years ago by • 0 • written 7.7 years ago by ▴ 40
19
votes
6
replies
23k
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How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq annotationdbi
updated 5.6 years ago by ★ 6.7k • written 5.7 years ago by ▴ 70
19
votes
1
reply
5.8k
views
Differences between limma voom E values and edgeR cpm values?
edgeR
updated 7.6 years ago by 45k • written 8.0 years ago by ▴ 70
19
votes
4
replies
4.6k
views
biomaRt no longer works with proxy after upgrade
biomart proxy rcurl
updated 6.5 years ago by ▴ 140 • written 6.5 years ago by ▴ 610
19
votes
10
replies
3.1k
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Do the outputs of Limma's competitive gene set methods (camera, romer) require a mutliple testing correction?
limma romer
updated 6.7 years ago by 45k • written 6.7 years ago by ▴ 40
19
votes
9
replies
26k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
updated 12 weeks ago by • 0 • written 8.5 years ago by ▴ 190
18
votes
37
replies
15k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
7.0 years ago • updated 6.8 years ago svlachavas ▴ 780
18
votes
6
replies
24k
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DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 7 weeks ago by • 0 • written 5.4 years ago by ▴ 50
18
votes
3
replies
1.7k
views
cameraPR vs geneSetTest and ROAST/CAMERA in general
limma voomwithqualityweights gene set analysis
updated 4.1 years ago by ★ 27k • written 4.1 years ago by ▴ 70
18
votes
12
replies
2.5k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 6.9 years ago by 37k • written 6.9 years ago by 7.8k
18
votes
17
replies
4.0k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 12 months ago by 37k • written 3.9 years ago by ▴ 20
18
votes
10
replies
5.1k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger estimatedispersions glm
updated 6.2 years ago by 45k • written 6.2 years ago by ▴ 140
18
votes
17
replies
2.2k
views
How to model a comparison between comparisons in edgeR?
edger rnaseq
updated 7.2 years ago by 7.8k • written 7.2 years ago by ▴ 60
18
votes
4
replies
536
views
`ggbio` package can't be loaded
ggbio
16 months ago Batool ▴ 370
18
votes
24
replies
11k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 15 months ago by • 0 • written 7.2 years ago by ▴ 110
18
votes
10
replies
12k
views
How do I merge a list of GRanges?
GenomicRanges
updated 3 months ago by ▴ 30 • written 5.9 years ago by ▴ 30
17
votes
8
replies
1.8k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 90
17
votes
5
replies
3.3k
views
Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
IRanges
updated 5.2 years ago by 25k • written 5.2 years ago by ▴ 10
1,000 results • Page 1 of 20
Recent ...
Replies
Answer: regression analysis for epic array methylation data using limma by Basti ▴ 280
Which package do you intend to use ? There are many tutorials in packages vignette that show you how to perform differential methylation an…
Comment: scRNASeq reference at a transcript level by Basti ▴ 280
I believe this question is not related to any Bioconductor package, I think the only solution to this question is to search yourself in Pub…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Upgrading the package solved the issue, thanks!
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2 by ATpoint ★ 1.2k
The error comes from the `mixsqp` package, see https://github.com/stephens999/ashr/issues/131. Upgrading the package to the most recent 0.3…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Thanks for the suggestion. I ran the following filtering criteria: ``` keep <- rowSums(counts(dds) >= 10) >= 5 dds <- dds[keep,] ``` It ga…
Votes
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: UniprotKB AC/ID to Entrez ID Conversion
edgeR: what to do with no replicates
Differential gene expression anlaysis?
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