Showing : DESeq2 • reset
13
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22
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27k
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DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 12 weeks ago by 42k • written 7.9 years ago by ▴ 30
0
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7
replies
460
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DESeq2 filtering vs edgeR filtering
DESeq2
9 weeks ago • updated 7 weeks ago fr8712ca-s • 0
14
votes
5
replies
22k
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Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by • 0 • written 8.4 years ago by ▴ 60
4
votes
13
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1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 42k • written 8 months ago by • 0
0
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4
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758
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
12 months ago sreeshmaraj72 • 0
0
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11
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1.3k
views
Unable to install DESeq2
DESeq2
updated 10 months ago by 65k • written 10 months ago by • 0
2
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3
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1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.4k • written 5 months ago by • 0
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 19 months ago by ▴ 20
1
vote
2
replies
712
views
DESeq2 batch design
DESeq2
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 10
1
vote
8
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1.6k
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 11 months ago by • 0
1
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2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
3
replies
481
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
0
votes
3
replies
514
views
Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 8 months ago by 65k • written 8 months ago by ▴ 30
1
vote
3
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509
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 4 months ago by • 0 • written 5 months ago by • 0
0
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5
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721
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout DESeq2
written 11 months ago by • 0
3
votes
2
replies
586
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
2
votes
6
replies
3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 10 months ago by • 0 • written 8.1 years ago by ▴ 20
0
votes
4
replies
399
views
Extract LRT results for each comparison
LRT DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
2
replies
605
views
DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 5 months ago by 42k • written 5 months ago by • 0
28
votes
21
replies
49k
views
deseq2 filter the low counts
deseq2 lowcount
updated 4 months ago by • 0 • written 9.2 years ago by ▴ 40
5
votes
18
replies
7.6k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 5 months ago by • 0 • written 2.3 years ago by • 0
1
vote
3
replies
611
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
2
votes
2
replies
336
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
12 weeks ago Hope ▴ 10
0
votes
17
replies
3.5k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 11 months ago by • 0 • written 6.6 years ago by • 0
0
votes
2
replies
568
views
Heat Map
ColData pheatmap DESeq2
written 11 months ago by • 0
0
votes
2
replies
501
views
plotCounts label each sample
p DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
0
votes
6
replies
921
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
6
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19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 19 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 6 months ago by • 0 • written 6.6 years ago by ▴ 60
0
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3
replies
421
views
LOG2FC DESEQ2
DESeq2
updated 3 months ago by 42k • written 3 months ago by • 0
0
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6
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297
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 15 days ago by ★ 1.4k • written 17 days ago by ▴ 130
0
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2
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326
views
Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 10 months ago by 65k • written 10 months ago by • 0
1
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3
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1.7k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 4.1 years ago by • 0
9
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5
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5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
1
vote
3
replies
440
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
10 months ago Ndimensional ▴ 20
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by ▴ 60
4
votes
7
replies
902
views
weird volcano plot
DESeq2
updated 10 weeks ago by • 0 • written 6 months ago by ▴ 10
0
votes
2
replies
351
views
Running DESeq on normalized data
deseq DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
4
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9
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1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
0
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5
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573
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Unexpected results for a differential expression analysis between males and females
DESeq2
updated 5 months ago by ★ 3.3k • written 5 months ago by • 0
3
votes
6
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23k
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Deseq: What does "BaseMean" mean?
deseq2
updated 4 months ago by • 0 • written 5.7 years ago by • 0
0
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4
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292
views
DEG with low counts
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 7 months ago by • 0 • written 5.4 years ago by • 0
1
vote
3
replies
914
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
updated 11 months ago by • 0 • written 12 months ago by • 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 4 weeks ago by • 0 • written 8.9 years ago by ▴ 30
0
votes
2
replies
168
views
DESeq2 v1.35.0
DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
2
votes
6
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384
views
Factor vs Character in design
DESeq2
10 weeks ago James Aiden • 0
2
votes
8
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1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
11 months ago Ndimensional ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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