Showing : DEseq • reset
1
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'Codetools' and 'mgcv' packages fail to update
package updates codetools deseq mgcv
updated 8.5 years ago by • 0 • written 8.5 years ago by • 0
1
vote
17
replies
5.0k
views
Filtering out tags with low counts in DESeq and EgdeR?
Normalization edgeR DESeq Normalization edgeR DESeq
12.4 years ago • updated 12.3 years ago Xiaohui Wu ▴ 280
1
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14
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9.7k
views
DESeq Error in round(assay(se)) : non-numeric argument to mathematical function
deseq rna-seq
8.5 years ago rodriguez.varenka • 0
2
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19
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2.4k
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phyloseq/DESeq gives negative transformed values
Microbiome DESeq Microbiome DESeq
updated 9.4 years ago by 40k • written 9.5 years ago by ▴ 130
0
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5
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2.1k
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EasyRNASeq issue (missing bai files)
GO PROcess DESeq easyRNASeq GO PROcess DESeq easyRNASeq
updated 11.2 years ago by ▴ 10 • written 11.2 years ago by ★ 1.2k
0
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7
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1.4k
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Differential expresson in more than 2 samples using NGS?
edgeR DESeq edgeR DESeq
13.1 years ago Xiaohui Wu ▴ 280
2
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7
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1.2k
views
Factoring analysis and better design
deseq2 deseq
7.1 years ago arabella23 • 0
0
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5
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1.7k
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edgeR - R script - results compared to DESeq
edgeR DESeq edgeR DESeq
updated 11.8 years ago by ▴ 40 • written 11.8 years ago by ▴ 40
2
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5
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3.8k
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Running DESeq with 1000 samples
DESeq DESeq
updated 8.3 years ago by • 0 • written 9.2 years ago by ★ 12k
0
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5
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1.8k
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DESeq and paired samples - pairing vs pooling
Cancer DESeq Cancer DESeq
updated 12.3 years ago by 48k • written 12.4 years ago by ▴ 20
0
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12
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2.7k
views
DEseq version and R version compatibility
DESeq DESeq
updated 11.0 years ago by ★ 1.7k • written 11.0 years ago by ▴ 280
0
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13
replies
6.1k
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Up & Downregulated genes using DESeq
DESeq DESeq
updated 11.5 years ago by ▴ 80 • written 11.5 years ago by ▴ 40
1
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15
replies
3.6k
views
DEseq for chip-seq data normalisation
DESeq DESeq2 DESeq DESeq2
updated 9.9 years ago by ▴ 90 • written 9.9 years ago by ▴ 170
1
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6
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3.2k
views
about DEseq for spike-in datasets
normalization deseq
8.1 years ago gan.haiyun • 0
26
votes
22
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17k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 6.2 years ago by ▴ 120 • written 8.0 years ago by ▴ 190
0
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8
replies
3.3k
views
DESeq and transcript-wise analysis
convert DESeq convert DESeq
11.6 years ago Elena Sorokin ▴ 150
0
votes
13
replies
2.9k
views
DESeq and number of replicates required for RNA-Seq
GO DESeq GO DESeq
updated 13.3 years ago by ★ 6.0k • written 13.3 years ago by ★ 3.4k
0
votes
7
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3.8k
views
edgeR/DESeq for ChIP-seq analysis
edgeR DESeq edgeR DESeq
updated 10.9 years ago by 48k • written 10.9 years ago by ▴ 240
0
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14
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2.0k
views
(no subject)
DESeq DESeq
updated 10.5 years ago by ▴ 20 • written 10.6 years ago by ▴ 30
5
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13
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5.1k
views
P values from Deseq Analysis
deseq
6.4 years ago Shrikant Pawar • 0
0
votes
3
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2.2k
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DESeq - working with more than 2 conditions
DESeq DESeq
updated 11.0 years ago by 13k • written 11.0 years ago by ▴ 140
25
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11
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7.2k
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Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 7.9 years ago by ★ 3.7k • written 7.9 years ago by ▴ 80
40
votes
44
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9.2k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 5.8 years ago by ▴ 60 • written 6.4 years ago by ▴ 10
7
votes
18
replies
7.5k
views
Differential expression analysis: Continuous variables
DESeq EdgeR limma
8.0 years ago Radek ▴ 90
9
votes
6
replies
8.9k
views
Error bars DESeq or DESeq2 fold change
rnaseq deseq2 deseq standard error confidence interval
updated 22 months ago by 40k • written 7.5 years ago by ▴ 10
14
votes
9
replies
13k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
8.7 years ago gavrielmatt ▴ 30
0
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3
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1.1k
views
question about DESeq: estimateDispersions
deseq
8.7 years ago yilongzou • 0
3
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11
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3.0k
views
DESeq function taking too long
deseq2 deseq factor rnaseq
updated 6.2 years ago by ★ 2.8k • written 6.2 years ago by ▴ 30
7
votes
12
replies
8.5k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2 deseq
updated 6.3 years ago by ▴ 60 • written 8.9 years ago by ▴ 20
0
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4
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1.2k
views
Using DESeq or EdgeR for Exon Differential Expression Analysis
Normalization edgeR DESeq Normalization edgeR DESeq
updated 12.5 years ago by ▴ 30 • written 12.5 years ago by ★ 6.0k
2
votes
4
replies
6.4k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing Alignment DESeq DESeq2 Sequencing Alignment DESeq DESeq2
updated 8.3 years ago by • 0 • written 9.3 years ago by ★ 12k
0
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7
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1.6k
views
No significant p-values
DESeq DESeq
updated 9.2 years ago by ▴ 330 • written 9.2 years ago by ★ 12k
0
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7
replies
3.1k
views
Repeated Measures mRNA expression analysis II
limma edgeR DESeq
updated 7.2 years ago by • 0 • written 10.2 years ago by ▴ 140
0
votes
3
replies
1.2k
views
DESeq variance question
edgeR DESeq edgeR DESeq
updated 11.8 years ago by 48k • written 11.8 years ago by ▴ 10
3
votes
5
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2.1k
views
DESeq on transcripts v/s genes
DESeq DESeq
updated 11.6 years ago by 13k • written 11.7 years ago by ▴ 410
0
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7
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2.4k
views
DESEQ ANODEV : A time course study
TimeCourse timecourse DESeq edgeR
updated 8.8 years ago by 48k • written 10.3 years ago by ▴ 20
0
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5
replies
2.0k
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normalization factors for ChIP/RNA-IP-seq data
edgeR DESeq edgeR DESeq
updated 6.4 years ago by • 0 • written 11.7 years ago by ▴ 370
0
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3
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2.1k
views
DESeq for an mRNA-seq time course
DESeq DESeq
11.7 years ago Elena Sorokin ▴ 150
0
votes
5
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2.1k
views
mRNA-seq cross-species analysis, is it possible?
Genetics Normalization Proteome DESeq Genetics Normalization Proteome DESeq
updated 12.1 years ago by ▴ 20 • written 12.2 years ago by ▴ 370
0
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3
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3.2k
views
phyloseq/DESeq gives negative transformed values
Microbiome Normalization Clustering DESeq DESeq2 Microbiome Normalization Clustering DESeq
updated 9.4 years ago by ▴ 130 • written 9.4 years ago by 40k
0
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5
replies
2.9k
views
DESeq2
Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn
updated 10.5 years ago by 40k • written 10.5 years ago by 13k
0
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4
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3.8k
views
Problem with DESeq : \"Error in FUN(newX[, i], ...) : could not find function \"locfunc\"\"
DESeq DESeq
updated 8.5 years ago by 13k • written 9.4 years ago by ★ 12k
0
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7
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1.1k
views
package to count read prior to DESeq?
DESeq DESeq
updated 11.6 years ago by ★ 3.5k • written 11.6 years ago by ▴ 280
0
votes
4
replies
2.0k
views
DESeq no recognizing row.names
DESeq DESeq
updated 10.3 years ago by 13k • written 10.3 years ago by ▴ 140
0
votes
9
replies
3.5k
views
DESeq vs DESeq2 have different DEGs results
DESeq DESeq2 DESeq DESeq2
9.4 years ago • updated 9.3 years ago Catalina Aguilar Hurtado ▴ 80
0
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6
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1.8k
views
Log transformation and left censoring
limma edgeR DESeq limma edgeR DESeq
updated 10.6 years ago by 48k • written 10.6 years ago by 13k
0
votes
2
replies
2.0k
views
DESeq and EdgeR log fold differences
Normalization edgeR DESeq Normalization edgeR DESeq
updated 10.8 years ago by 48k • written 10.8 years ago by ▴ 40
0
votes
5
replies
1.4k
views
filtering before using DESeq
DESeq DESeq
updated 10.8 years ago by 13k • written 10.8 years ago by ▴ 190
0
votes
3
replies
15k
views
DESeq - plotPCA
DESeq DESeq
updated 10.6 years ago by ★ 3.7k • written 10.6 years ago by ★ 12k
0
votes
2
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1.3k
views
DESeq - Estimating Dispersion with Technical Replicates
GLAD DESeq GLAD DESeq
updated 11.0 years ago by 13k • written 11.0 years ago by ▴ 20
50 results • Page 1 of 1
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Replies
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
Thank you, I have a very clear understanding of the situation. > COO_Sparse_HDF5RealizationSink(), writeHDF5SparseArray(), COO_H5SparseArr…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
There are a few places inside my `DelayedTensor` package that use `SparseArraySeed`. Will these stop working in next coming BioC 3.18, whe…
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
No. But I will need to modify the `write_block()` method for TENxRealizationSink implemented in **HDF5Array** to make it handle blocks that…
Answer: ''Model_Matrix'' error by Gordon Smyth 48k
This is actually an error message from base R rather than from limma. The error says that `Group` contains 0 or 1 levels, so your assumptio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I don't know the details but do you mean using HDF5RealizationSink or TENxRealizationSink will make it possible to writing sparse multi-d…
Votes
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
Awards • All
Popular Question to Koki ▴ 10
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Popular Question to sohail.mbio ▴ 10
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