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 9 weeks ago by 41k • written 7.9 years ago by ▴ 30
0
votes
7
replies
424
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DESeq2 filtering vs edgeR filtering
DESeq2
7 weeks ago • updated 5 weeks ago fr8712ca-s • 0
0
votes
4
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738
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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
5.3k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.2 years ago by • 0
14
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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
0
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11
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1.3k
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Unable to install DESeq2
DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
4
votes
13
replies
1.3k
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Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
1
vote
11
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1.0k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
3
replies
498
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Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 7 months ago by 65k • written 7 months ago by ▴ 30
1
vote
3
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584
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
2
votes
2
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305
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locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
9 weeks ago Hope ▴ 10
0
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3
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451
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
0
votes
6
replies
838
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 4 months ago by • 0 • written 2.3 years ago by • 0
4
votes
9
replies
1.3k
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RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
1
vote
8
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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
1
vote
3
replies
393
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
0
votes
4
replies
367
views
Extract LRT results for each comparison
LRT DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
8
votes
12
replies
2.6k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by 41k • written 12 months ago by ▴ 90
0
votes
2
replies
574
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
3
replies
891
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
0
votes
5
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700
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
0
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4
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674
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Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 4 months ago by • 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
2
votes
6
replies
335
views
Factor vs Character in design
DESeq2
8 weeks ago James Aiden • 0
3
votes
2
replies
558
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
0
votes
2
replies
550
views
Heat Map
ColData pheatmap DESeq2
written 10 months ago by • 0
0
votes
9
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2.5k
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
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 18 months ago by ▴ 20
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
10 months ago Ndimensional ▴ 20
1
vote
3
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1.7k
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How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 4.1 years ago by • 0
0
votes
2
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313
views
Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
2
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334
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Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
2
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6
replies
3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 9 months ago by • 0 • written 8.0 years ago by ▴ 20
0
votes
3
replies
366
views
LOG2FC DESEQ2
DESeq2
updated 3 months ago by 41k • written 3 months ago by • 0
9
votes
5
replies
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
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by • 0 • written 4.6 years ago by ▴ 10
4
votes
7
replies
856
views
weird volcano plot
DESeq2
updated 8 weeks ago by • 0 • written 5 months ago by ▴ 10
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 • updated 9 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
0
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2
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475
views
plotCounts label each sample
p DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
28
votes
21
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48k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.2 years ago by ▴ 40
0
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5
replies
530
views
Unexpected results for a differential expression analysis between males and females
DESeq2
updated 4 months ago by ★ 3.3k • 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
1
vote
3
replies
457
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 4 months ago by • 0 • written 4 months ago by • 0
0
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4
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253
views
DEG with low counts
DESeq2
updated 12 days ago by 41k • written 17 days ago by • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 13 days ago by • 0 • written 8.8 years ago by ▴ 30
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
2
replies
545
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
Recent ...
Replies
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM() by James W. MacDonald 65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Votes
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Awards • All
Scholar to Rory Stark ★ 5.2k
Popular Question to tangming2005 ▴ 190
Popular Question to Ian D. ▴ 70
Popular Question to junhui.li11 • 0
Scholar to James W. MacDonald 65k
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