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Showing :
contrasts
•
reset
2
votes
7
replies
549
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
3 months ago • updated 8 weeks ago
Nicole
• 0
0
votes
3
replies
339
views
limma voom contrasts
contrasts
limma
voom
updated 5 months ago by
Gordon Smyth
46k • written 5 months ago by
S T
▴ 80
0
votes
1
reply
229
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 6 months ago by
Michael Love
37k • written 6 months ago by
Mir
• 0
0
votes
2
replies
397
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
11 months ago
James
• 0
0
votes
3
replies
328
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 12 months ago by
Kevin Blighe
3.6k • written 12 months ago by
Mir
• 0
2
votes
8
replies
719
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
15 months ago • updated 14 months ago
Jane
• 0
3
votes
8
replies
570
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 2.7 years ago by
James W. MacDonald
60k • written 2.7 years ago by
s.connell
• 0
0
votes
1
reply
498
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2
contrasts
reference level
updated 2.7 years ago by
Michael Love
37k • written 2.7 years ago by
ananda2
• 0
0
votes
0
replies
289
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
2.7 years ago
ingerslev
• 0
0
votes
1
reply
638
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 2.7 years ago by
Michael Love
37k • written 2.7 years ago by
ananda2
• 0
2
votes
3
replies
668
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 2.7 years ago by
Michael Love
37k • written 2.7 years ago by
Keith Hughitt
▴ 170
0
votes
4
replies
473
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 2.9 years ago by
Gordon Smyth
46k • written 2.9 years ago by
uridavid.akavia
• 0
0
votes
1
reply
365
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 3.2 years ago by
Michael Love
37k • written 3.2 years ago by
kehoe
• 0
3
votes
5
replies
746
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 3.4 years ago by
Aaron Lun
★ 27k • written 3.4 years ago by
Pietro
▴ 30
2
votes
6
replies
560
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 3.5 years ago by
Gordon Smyth
46k • written 3.5 years ago by
Maiv
• 0
15 results • Page
1 of 1
Recent ...
Replies
Comment: DEXseq error unable to find an inherited method for function NSBS for signature
by
ta_awwad
▴ 10
Hi there, did you manage to solve this problem? thanks TA
Comment: Error in Create switchAnalyzeRlist
by
k.vitting.seerup
▴ 120
I just double checked and the fasta files found [here][1] should work. Please also take a look at [this][2] if you want to use Ensembl. …
Answer: Correlation between two different datasets: between results of RNAseq and absenc
by
Michael Love
37k
Re: LFC, if you are working with this and then downstream analysis, I'd recommend `lfcShrink` if you aren't already using this. It will shr…
Answer: Strange Dispersion plot
by
Michael Love
37k
This indeed looks strange, I would immediately suspect some weird batch effects. Try all kinds of diagnostic plots like, boxplot, PCA, corr…
Answer: Correlation between CpG methylation and gene expression from DESeq2-> Normalizat
by
Michael Love
37k
In this case, can you say why you want to normalize for gene length? In our tximport/tximeta pipeline, it would correct for differential ge…
Votes
Answer: Error in Create switchAnalyzeRlist
Answer: Error in Create switchAnalyzeRlist
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
Answer: the difference between getGEO and getGEOSuppFiles
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