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DEGS
•
reset
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 5.9 years ago by
aishu.jp
▴ 30
0
votes
3
replies
819
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
Michael Love
43k • written 2.3 years ago by
Mike
• -60
-6
votes
4
replies
1000
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 2.7 years ago by
Gordon Smyth
52k • written 2.7 years ago by
RR
• 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
replies
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
Gordon Smyth
52k • written 3.4 years ago by
Ming
▴ 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
Kevin Blighe
★ 4.0k • written 3.5 years ago by
robledoj13
• 0
0
votes
2
replies
1.2k
views
Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2
Nullcook'svalues
2x3
DEGs
3.7 years ago
andreia
▴ 10
4
votes
5
replies
1.6k
views
DEseq2 results
heatmaps
DEGs
PCA
updated 3.8 years ago by
Kevin Blighe
★ 4.0k • written 3.8 years ago by
MOHAMMAD
• 0
2
votes
2
replies
1.2k
views
Design formula for pairwise comparison of experimental setup with multiple factors
DEGs
DESeq2
4.0 years ago
2021yearsold
• 0
0
votes
1
reply
1000
views
mircomb analysis from deg's list
mircomb
mrna
mirna
degs
interaction
4.5 years ago
andreia
▴ 10
0
votes
2
replies
958
views
mirna-mrna interation mircomb (from DEGs and DEMs lists)
deseq2
mircomb
degs
dems
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
andreia
▴ 10
0
votes
1
reply
1.1k
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler
Bioconductor
R
DEGs
4.5 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
Gordon Smyth
52k • written 4.9 years ago by
anikng
▴ 10
2
votes
4
replies
1.2k
views
How to make grouping and contrast for multfactor design?
edger
DEGs
5.0 years ago • updated 4.9 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
Michael Love
43k • written 5.1 years ago by
gmchaput
• 0
0
votes
2
replies
4.6k
views
Heatmap of selected genes
heatmap
DEGs
RNAseq
DESeq2
updated 5.4 years ago by
mikhael.manurung
▴ 280 • written 5.4 years ago by
danikadigiacomo
• 0
4
votes
3
replies
1.3k
views
Differential profile for only one normal - tumor pair
edger
degs
paired design
updated 6.5 years ago by
Gordon Smyth
52k • written 6.5 years ago by
takumima
▴ 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
Gordon Smyth
52k • written 6.9 years ago by
lawarde.ankita1
▴ 30
3
votes
1
reply
1.2k
views
Common dispersion value using edgeR for DEGs analysis
edgeR
DEGS
common disperion
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
baus87
• 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
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Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Hervé Pagès
16k
> I have requested gDNAx developers for a feature request to turn off seqlevelsStyle(txdb) Yes, that's the right course of action. `seqlev…
Comment: ISO a solution to rank-order introns by transcript
by
mat149
▴ 80
Hey, In revisiting this question, the following code works for the '+' strand. I am having issues with demarcating intron rank by transcri…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
Gordon Smyth
52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
anna.cot.anna.cot
▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Tim Peters
▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Votes
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Answer: nightmare to make custom txdb for genomes from ToxoDB
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