Showing : DEGs • reset
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.0 years ago by ▴ 30
0
votes
3
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828
views
code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2 Complicated.contrast DEGs
updated 2.3 years ago by 43k • written 2.3 years ago by • -60
-6
votes
4
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1.0k
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast edgeR DEGs
2.3 years ago Mike • -60
2
votes
3
replies
1.1k
views
Classic or GLM approach in edgeR, Why do I got less DEG in GLM approach?
edgeR DEGs
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
0
votes
2
replies
1.0k
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
2.9 years ago Raito92 ▴ 60
0
votes
3
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1.2k
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
updated 2.8 years ago by 52k • written 3.4 years ago by ▴ 380
0
votes
20
replies
2.9k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2 DEGs
3.5 years ago • updated 3.4 years ago Ming ▴ 380
2
votes
1
reply
7.2k
views
EnhancedVolcano Label Question
RNASeq EnhancedVolcano DEGs
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
0
votes
2
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1.2k
views
Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2 Nullcook'svalues 2x3 DEGs
3.8 years ago andreia ▴ 10
4
votes
5
replies
1.6k
views
DEseq2 results
heatmaps DEGs PCA
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
2
votes
2
replies
1.3k
views
Design formula for pairwise comparison of experimental setup with multiple factors
DEGs DESeq2
4.0 years ago 2021yearsold • 0
0
votes
1
reply
1.0k
views
mircomb analysis from deg's list
mircomb mrna mirna degs interaction
4.5 years ago andreia ▴ 10
0
votes
2
replies
964
views
mirna-mrna interation mircomb (from DEGs and DEMs lists)
deseq2 mircomb degs dems
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 10
0
votes
1
reply
1.1k
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler Bioconductor R DEGs
4.6 years ago tpm • 0
3
votes
2
replies
3.0k
views
How to deal with elimination of genes when using filterByExpr function?
edger DEGs normalization
updated 4.9 years ago by 52k • written 4.9 years ago by ▴ 10
2
votes
4
replies
1.2k
views
How to make grouping and contrast for multfactor design?
edger DEGs
5.0 years ago anikng ▴ 10
2
votes
3
replies
1.2k
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2 rrpp DEGs RNAseq
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
votes
2
replies
4.6k
views
Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 5.4 years ago by ▴ 280 • written 5.4 years ago by • 0
4
votes
3
replies
1.4k
views
Differential profile for only one normal - tumor pair
edger degs paired design
updated 6.5 years ago by 52k • written 6.5 years ago by ▴ 10
3
votes
5
replies
2.4k
views
DEGs of microarray Data and hierarchical clustering and visualizing using heatmap
limma heatmap DEGs
updated 6.9 years ago by 52k • written 6.9 years ago by ▴ 30
3
votes
1
reply
1.2k
views
Common dispersion value using edgeR for DEGs analysis
edgeR DEGS common disperion
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
6
votes
4
replies
3.0k
views
Identification of DEGs through limma analysis
limma microarray DEGs p values lfc
7.5 years ago rkp • 0
22 results • Page 1 of 1
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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