Showing : deseq2 • reset
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 10 weeks ago by 41k • written 7.9 years ago by ▴ 30
0
votes
7
replies
432
views
DESeq2 filtering vs edgeR filtering
DESeq2
7 weeks ago • updated 5 weeks ago fr8712ca-s • 0
0
votes
4
replies
743
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
4
votes
13
replies
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by • 0 • written 8.4 years ago by ▴ 60
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by 65k • written 9 months ago by • 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
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
6
replies
345
views
Factor vs Character in design
DESeq2
8 weeks ago James Aiden • 0
0
votes
6
replies
854
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
votes
5
replies
706
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
1
vote
3
replies
596
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 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
458
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
1
vote
3
replies
895
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 12 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
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
3
votes
2
replies
561
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
Accounting for technical replicates in DESeq2
DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by • 0
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
votes
5
replies
540
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
1
vote
3
replies
472
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 4 months ago by • 0 • written 4 months ago by • 0
0
votes
2
replies
82
views
DESeq2 v1.35.0
DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
2
replies
1.4k
views
about baseMean in DEseq2
DESeq2
written 2.8 years ago by ▴ 670
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
0
votes
4
replies
683
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 4 months ago by • 0
2
votes
6
replies
3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 9 months ago by • 0 • written 8.0 years ago by ▴ 20
2
votes
2
replies
313
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
10 weeks ago Hope ▴ 10
0
votes
9
replies
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
0
votes
2
replies
557
views
Heat Map
ColData pheatmap DESeq2
written 10 months ago by • 0
0
votes
2
replies
479
views
plotCounts label each sample
p DESeq2
updated 10 months ago by ★ 4.1k • written 10 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
0
votes
6
replies
172
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 1 day ago by ★ 1.3k • written 2 days ago by ▴ 130
0
votes
2
replies
314
views
Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 9 months ago by 65k • written 9 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
0
votes
3
replies
372
views
LOG2FC DESEQ2
DESeq2
updated 3 months ago by 41k • written 3 months ago by • 0
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 4 days ago by • 0 • written 4.6 years ago by ▴ 10
1
vote
3
replies
404
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
4
votes
7
replies
866
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 Ndimensional ▴ 20
0
votes
2
replies
340
views
Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
4
replies
373
views
Extract LRT results for each comparison
LRT DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.2 years ago by ▴ 40
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 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
2
replies
582
views
DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 4 months ago by 41k • written 4 months ago by • 0
0
votes
4
replies
263
views
DEG with low counts
DESeq2
updated 15 days ago by 41k • written 20 days ago by • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 16 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
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
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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