67
votes
8
replies
56k
views
conceptual question about FDR, FDR adjusted p-value and q-value
fdr qvalue
updated 7.8 years ago by 51k • written 11.6 years ago by ▴ 440
52
votes
20
replies
45k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 8.2 years ago by • 0 • written 8.6 years ago by ▴ 110
44
votes
29
replies
12k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db pathview
updated 3.3 years ago by ▴ 130 • written 3.3 years ago by ▴ 160
41
votes
44
replies
11k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 6.6 years ago by ▴ 60 • written 7.2 years ago by ▴ 10
34
votes
21
replies
15k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
9.9 years ago • updated 22 months ago Michael Love 42k
33
votes
16
replies
41k
views
Differential expression analysis starting from TPM data
R TPM
updated 7.0 years ago by 51k • written 7.0 years ago by ▴ 90
32
votes
10
replies
39k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
updated 15 months ago by • 0 • written 10.7 years ago by ▴ 250
32
votes
16
replies
18k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.3 years ago by ▴ 20 • written 8.0 years ago by ▴ 190
32
votes
0
replies
39k
views
limma moderated t-statistics and B-statistics
Microarray limma
19.9 years ago • updated 3.8 years ago Gordon Smyth 51k
28
votes
8
replies
12k
views
Removing continuous covariate effects in limma analysis
limma microarray
updated 6.9 years ago by 51k • written 9.3 years ago by ▴ 160
28
votes
25
replies
6.1k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 7.0 years ago by ▴ 10 • written 7.4 years ago by ▴ 100
28
votes
21
replies
51k
views
deseq2 filter the low counts
deseq2 lowcount
updated 6 months ago by • 0 • written 9.4 years ago by ▴ 40
28
votes
43
replies
8.8k
views
Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
findoverlaps granges
updated 8.3 years ago by 25k • written 8.4 years ago by ▴ 80
27
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 9 months ago by ▴ 10 • written 6.8 years ago by ▴ 40
27
votes
13
replies
17k
views
problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignments’ , ‘ShortRead’ on macOS Big Sur using R 4.1.0
dada2
updated 18 months ago by • 0 • written 3.2 years ago by ▴ 60
27
votes
21
replies
24k
views
Mapping genome regions to gene symbols
tcga cnv gene symbol coordinate
updated 20 months ago by 66k • written 9.3 years ago by ▴ 60
26
votes
22
replies
19k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 7.1 years ago by ▴ 120 • written 8.9 years ago by ▴ 190
26
votes
17
replies
7.6k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 3.2 years ago by 42k • written 6.1 years ago by ▴ 40
25
votes
37
replies
11k
views
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 7.5 years ago by 51k • written 7.5 years ago by ▴ 830
25
votes
11
replies
8.0k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 8.7 years ago by ★ 3.7k • written 8.7 years ago by ▴ 80
25
votes
7
replies
10k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 6.8 years ago by 51k • written 6.8 years ago by ▴ 20
25
votes
7
replies
15k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 7.8 years ago by ★ 3.7k • written 7.8 years ago by ▴ 30
25
votes
9
replies
7.1k
views
voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 9.5 years ago by 51k • written 9.5 years ago by ▴ 40
24
votes
12
replies
12k
views
Nanostring analysis with limma
nanostring limma
updated 9.2 years ago by ▴ 20 • written 9.3 years ago by ▴ 370
24
votes
6
replies
40k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 2.3 years ago by ▴ 20 • written 7.5 years ago by ▴ 50
24
votes
11
replies
19k
views
when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
limma voom limma voom rna-seq quantile normalization
updated 8.5 years ago by 51k • written 8.5 years ago by ▴ 50
23
votes
11
replies
2.1k
views
Bioconductor vs BioConductor
project
updated 4.2 years ago by 51k • written 4.2 years ago by ▴ 40
22
votes
15
replies
8.1k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 8 months ago by ▴ 10 • written 2.3 years ago by ▴ 50
22
votes
4
replies
10k
views
Correct assumptions of using limma moderated t-test
limma statistical inference variance test bioconductor
updated 9.2 years ago by 51k • written 9.2 years ago by ▴ 830
22
votes
13
replies
27k
views
gene dispersion, what does it mean?
gener rnaseq
updated 16 months ago by 51k • written 8.7 years ago by ▴ 80
22
votes
10
replies
7.6k
views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges chippeakanno
updated 7.4 years ago by ▴ 10 • written 7.4 years ago by ▴ 80
22
votes
12
replies
26k
views
New function lfcShrink() in DESeq2
deseq2
updated 5.0 years ago by • 0 • written 7.2 years ago by 42k
22
votes
8
replies
4.4k
views
Limma camera function never gives any differentially expressed gene sets
limma
updated 7.0 years ago by • 0 • written 9.0 years ago by ▴ 420
21
votes
5
replies
15k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 9.2 years ago by 51k • written 10.2 years ago by ▴ 190
21
votes
1
reply
7.9k
views
Differences between limma voom E values and edgeR cpm values?
edgeR
updated 9.8 years ago by 51k • written 10.2 years ago by ▴ 90
21
votes
24
replies
13k
views
Problem with biomart's listMarts function
biomart bug
updated 8.2 years ago by ▴ 470 • written 8.7 years ago by ★ 2.1k
21
votes
34
replies
8.9k
views
Biomart error when updating to R 4.0.2
Biomart
updated 3.8 years ago by ★ 6.5k • written 3.8 years ago by ▴ 40
21
votes
10
replies
8.9k
views
Tutorial: Bioconductor on Coursera
mooc Tutorial
updated 6.3 years ago by • 0 • written 8.9 years ago by ★ 6.5k
21
votes
13
replies
16k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger rnaseq
updated 9.8 years ago by 66k • written 9.8 years ago by ▴ 50
20
votes
13
replies
3.6k
views
News: markdown is coming to the support site
markdown News
7.0 years ago • updated 6.4 years ago Lucas Schiffer ▴ 240
19
votes
7
replies
13k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2 ensembl
updated 6.5 years ago by 66k • written 6.5 years ago by ▴ 160
19
votes
8
replies
3.4k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 6.3 years ago by 21k • written 6.3 years ago by ▴ 120
19
votes
6
replies
37k
views
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq annotationdbi
updated 7.8 years ago by ★ 6.8k • written 7.8 years ago by ▴ 70
19
votes
10
replies
19k
views
How do I merge a list of GRanges?
GenomicRanges
updated 2.5 years ago by ▴ 40 • written 8.1 years ago by ▴ 40
19
votes
10
replies
4.3k
views
Do the outputs of Limma's competitive gene set methods (camera, romer) require a mutliple testing correction?
limma romer
updated 8.9 years ago by 51k • written 8.9 years ago by ▴ 40
19
votes
4
replies
8.4k
views
Confidence intervals on edgeR logFC
edgeR statistics confidence interval
updated 8.3 years ago by • 0 • written 9.8 years ago by ▴ 40
19
votes
4
replies
5.7k
views
biomaRt no longer works with proxy after upgrade
biomart proxy rcurl
updated 8.7 years ago by ▴ 140 • written 8.7 years ago by ▴ 660
19
votes
15
replies
60k
views
DESeq2 output explanation
deseq deseq2
updated 2.7 years ago by 42k • written 9.7 years ago by ▴ 100
18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
9.2 years ago • updated 9.0 years ago svlachavas ▴ 830
18
votes
17
replies
4.3k
views
How to model a comparison between comparisons in edgeR?
edger rnaseq
updated 9.4 years ago by ★ 7.9k • written 9.4 years ago by ▴ 60
45,886 results • Page 1 of 918
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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