Showing : Deseq2 • reset
0
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7
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397
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DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 23 days ago fr8712ca-s • 0
13
votes
22
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26k
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DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 8 weeks ago by 41k • written 7.8 years ago by ▴ 30
0
votes
11
replies
1.2k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 6 months ago by 41k • written 7 months ago by • 0
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 8 months ago by • 0 • written 8.3 years ago by ▴ 60
0
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4
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725
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
1
vote
9
replies
5.2k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.1 years ago by • 0
0
votes
3
replies
430
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
4 months ago Karthik • 0
1
vote
3
replies
563
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 3 months ago by • 0
8
votes
7
replies
1.7k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 9 months ago by ▴ 20 • written 18 months ago by ▴ 20
0
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2
replies
1.3k
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about baseMean in DEseq2
DESeq2
written 2.7 years ago by ▴ 670
0
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4
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647
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Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 3 months ago by • 0
2
votes
2
replies
285
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
7 weeks ago Hope ▴ 10
0
votes
2
replies
530
views
Heat Map
ColData pheatmap DESeq2
written 10 months ago by • 0
1
vote
3
replies
436
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 3 months ago by • 0 • written 4 months ago by • 0
0
votes
3
replies
352
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
1
vote
3
replies
858
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
updated 10 months ago by • 0 • written 11 months ago by • 0
2
votes
8
replies
1.0k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
10 months ago Ndimensional ▴ 20
2
votes
9
replies
1.1k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
9 months ago Ndimensional ▴ 20
0
votes
4
replies
355
views
Extract LRT results for each comparison
LRT DESeq2
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
4
votes
9
replies
1.2k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
8 months ago Luca • 0
0
votes
2
replies
546
views
DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 4 months ago by 41k • written 4 months ago by • 0
1
vote
5
replies
1.4k
views
How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
12 months ago • updated 11 months ago Weiqian ▴ 10
1
vote
8
replies
1.5k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 10 months ago by • 0
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 6 months ago by • 0 • written 5.4 years ago by • 0
0
votes
5
replies
691
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout DESeq2
written 10 months ago by • 0
3
votes
2
replies
539
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 4 months ago by 65k • written 4 months ago by • 0
2
votes
6
replies
315
views
Factor vs Character in design
DESeq2
6 weeks ago James Aiden • 0
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 10 months ago by • 0 • written 6.6 years ago by • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
0
votes
2
replies
604
views
Why my log2fcs are too high?
DESeq2 SingleCell log2FC
11 months ago paria.alipour • 0
0
votes
2
replies
307
views
Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
9
votes
5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 4 months ago by 50k • written 8.2 years ago by ▴ 90
0
votes
2
replies
318
views
Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
1
vote
3
replies
1.7k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 4.1 years ago by • 0
2
votes
6
replies
2.9k
views
DESeq2 Dispersion Per Condition
deseq2
updated 9 months ago by • 0 • written 8.0 years ago by ▴ 20
0
votes
3
replies
341
views
LOG2FC DESEQ2
DESeq2
updated 11 weeks ago by 41k • written 11 weeks ago by • 0
5
votes
12
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 3 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
9
replies
2.4k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 5 months ago by • 0 • written 6.5 years ago by ▴ 60
4
votes
7
replies
829
views
weird volcano plot
DESeq2
updated 6 weeks ago by • 0 • written 5 months ago by ▴ 10
0
votes
2
replies
460
views
plotCounts label each sample
p DESeq2
updated 9 months ago by ★ 4.0k • written 9 months ago by • 0
1
vote
8
replies
2.7k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.1 years ago by ▴ 60
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 11 months ago by ★ 4.0k • written 7.7 years ago by ▴ 20
8
votes
12
replies
2.5k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by 41k • written 11 months ago by ▴ 90
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.1 years ago by ▴ 40
0
votes
5
replies
508
views
Unexpected results for a differential expression analysis between males and females
DESeq2
updated 4 months ago by ★ 3.2k • written 4 months ago by • 0
3
votes
6
replies
22k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 3 months ago by • 0 • written 5.6 years ago by • 0
0
votes
3
replies
173
views
DEG with low counts
DESeq2
4 days ago • updated 2 days ago Rajat • 0
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 20 hours ago by • 0 • written 8.8 years ago by ▴ 30
0
votes
2
replies
528
views
Accounting for technical replicates in DESeq2
DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by • 0
50 results • Page 1 of 1
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Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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