Showing : Contrasts • reset
3
votes
3
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775
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 10 months ago by ★ 4.7k • written 10 months ago by ▴ 10
2
votes
3
replies
759
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 11 months ago by 52k • written 11 months ago by • 0
0
votes
3
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1.2k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 20 months ago by 68k • written 20 months ago by • 0
1
vote
2
replies
791
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
21 months ago jovel_juan ▴ 30
3
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6
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1.5k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.2 years ago mohammedtoufiq91 ▴ 10
1
vote
3
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905
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
3
votes
8
replies
4.7k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.8 years ago by ▴ 10
0
votes
3
replies
1.9k
views
limma voom contrasts
contrasts limma voom
updated 3.0 years ago by 52k • written 3.0 years ago by ▴ 90
0
votes
1
reply
949
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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2
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1.2k
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
3.5 years ago James • 0
0
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3
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1.4k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
2
votes
8
replies
2.7k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.8 years ago Jane ▴ 10
3
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8
replies
1.6k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
votes
1
reply
1.3k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
0
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0
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881
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.2 years ago ingerslev • 0
0
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1
reply
1.4k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
3
replies
1.7k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 180
0
votes
4
replies
1.3k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 5.4 years ago by 52k • written 5.4 years ago by • 0
0
votes
1
reply
865
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
votes
5
replies
1.8k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 40
2
votes
6
replies
1.4k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 6.1 years ago by 52k • written 6.1 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Answer: Differential expression of proteins using somascan data by James W. MacDonald 68k
Providing a bunch of code but not the output is not very helpful. Ideally you would just provide ``` nrow(design) ncol(protein_data_lo…
Comment: Surprising behavior for DEXseq dispersion estimate plot? by Elijah • 0
Hi Snow, Thanks for your comment! I didn't do any normalization of the counts prior to the DEXseq pipeline - I've only been using the inte…
Comment: Using tximport for kallisto aligned TOIL data by Nicholas • 0
Sorry, I misspoke. The data was from the TOIL project and was aligned using kallisto. It was accessed from the UCSC XENA browser. I updated…
Comment: Using tximport for kallisto aligned recount2 data by ATpoint ★ 4.7k
recount 2 does not use kallisto, does it? And recount does offer genelevel counts, so what's the point?
Comment: Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package by Yao Lipu • 0
Thank you for your help! Your explanation was very clear and really helped me solve my issue. I truly appreciate your time and effort!
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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