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DESE
•
reset
2
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2
replies
473
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq
DESeq2
dese
3 months ago
BioinfGuru
▴ 70
0
votes
1
reply
339
views
collapseReplicates dimension error
DESeq2
Dese
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Léa
• 0
0
votes
3
replies
493
views
DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2
dese
written 9 months ago by
Xu
• 0
0
votes
2
replies
517
views
Cross-species analysis using DESeq2 - size factor computation
dese
DESeq2
10 months ago • updated 9 months ago
pl23
• 0
0
votes
2
replies
762
views
Linear Model Fitting and Colinearity
dese
DESeq2
11 months ago
Hugo
• 0
0
votes
5
replies
1.1k
views
DESeq2 analysis
DESe
DESeq2
16 months ago
Adèle
• 0
0
votes
2
replies
1.5k
views
Handling NA's in Deseq2
Dese
DESeq2
18 months ago • updated 17 months ago
Asger Mølgaard
• 0
2
votes
17
replies
2.4k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 18 months ago by
Michael Love
43k • written 18 months ago by
Alina
• 0
4
votes
5
replies
1.6k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 5 months ago by
ij283
• 0 • written 19 months ago by
Bernardo
▴ 10
3
votes
3
replies
1.1k
views
Merging two plated in R
dese
DESeq2
updated 2.5 years ago by
James W. MacDonald
67k • written 2.5 years ago by
lmrogers34
▴ 10
0
votes
5
replies
3.9k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
DESE
DESeq2
updated 2.5 years ago by
Basti
▴ 780 • written 2.5 years ago by
Maryam.sed1400
• 0
1
vote
3
replies
1.7k
views
ERROR: unable to find an inherited method for function ‘dispersions<-’ for signature ‘"DESeqDataSet",
DESeq2
dese
2.8 years ago
aedavids
▴ 20
0
votes
2
replies
1.0k
views
DESeq2 ratio of ratios and p-value
DESeq2
dese
3.1 years ago
wilfried.guiblet
• 0
0
votes
2
replies
766
views
where the gene is overexpressed and down regulated while doing DESeq2 analysis
DESe
DESeq2
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
Dinesh
• 0
2
votes
3
replies
1.2k
views
Single sided P-value for DESeq2 Likelihood Ratio Test
DESeq2
DESe
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
glennli
• 0
0
votes
2
replies
985
views
Effect of within-group variation on gene expression analysis
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
hpapoli
• 0
16 results • Page
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Recent ...
Replies
Comment: Deseq2 res Function
by
James W. MacDonald
67k
In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…
Answer: Struggle with the replicates of epic array data
by
James W. MacDonald
67k
You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …
Comment: Identifying potentially associated gene set to drug response using GSVA
by
Robert Castelo
★ 3.4k
So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…
Answer: Deseq2 res Function
by
Michael Love
43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR
by
Gordon Smyth
51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Votes
Comment: Is it recommended to analyze different tissues together when using edgeR
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
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