Showing : Deseq2 • reset
13
votes
22
replies
26k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 9 weeks ago by 41k • written 7.8 years ago by ▴ 30
0
votes
7
replies
412
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 4 weeks ago fr8712ca-s • 0
0
votes
4
replies
732
views
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 6.1 years ago by • 0
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 8 months ago by • 0 • written 8.4 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
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
0
votes
6
replies
814
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
2
votes
2
replies
296
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
8 weeks ago Hope ▴ 10
1
vote
11
replies
997
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
0
votes
4
replies
658
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 4 months ago by • 0
2
votes
6
replies
327
views
Factor vs Character in design
DESeq2
7 weeks ago James Aiden • 0
0
votes
2
replies
542
views
Heat Map
ColData pheatmap DESeq2
written 10 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
1
vote
3
replies
878
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
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 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 2.2 years ago by • 0
1
vote
3
replies
383
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks ago by • 0
0
votes
2
replies
540
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
2.7k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.1 years ago by ▴ 60
0
votes
5
replies
520
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
447
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
1.4k
views
about baseMean in DEseq2
DESeq2
written 2.7 years ago by ▴ 670
0
votes
5
replies
696
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
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
3
replies
571
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
3
votes
2
replies
549
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
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
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
3
replies
442
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago • updated 4 months ago Karthik • 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
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
2
replies
310
views
Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
2
replies
329
views
Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.0k • 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
0
votes
3
replies
356
views
LOG2FC DESEQ2
DESeq2
updated 12 weeks ago by 41k • written 12 weeks 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
16
replies
2.3k
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 41k • written 4.6 years ago by ▴ 10
4
votes
7
replies
843
views
weird volcano plot
DESeq2
updated 7 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
9 months ago Ndimensional ▴ 20
0
votes
2
replies
465
views
plotCounts label each sample
p DESeq2
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
0
votes
4
replies
359
views
Extract LRT results for each comparison
LRT DESeq2
updated 6 months ago by ★ 4.0k • written 6 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
1.2k
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
563
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
233
views
DEG with low counts
DESeq2
updated 7 days ago by 41k • written 11 days ago by • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 8 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
615
views
Why my log2fcs are too high?
DESeq2 SingleCell log2FC
12 months ago paria.alipour • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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