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ExperimentalDesign
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Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 6 months ago by
swbarnes2
★ 1.3k • written 6 months ago by
Sam
• 0
2
votes
1
reply
635
views
edgeR with Successive Differences Contrast Coding?
hypothesisTesting
contrastCoding
edger
ExperimentalDesign
expressionDifferences
updated 12 months ago by
Gordon Smyth
50k • written 12 months ago by
Hannes
• 0
1
vote
1
reply
697
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 19 months ago by
ATpoint
★ 4.0k • written 19 months ago by
Mohamed
▴ 30
1
vote
2
replies
1.1k
views
How to properly use DESeq2 for an experiment
ExperimentalDesign
RNASeq
DifferentialExpression
DESeq2
updated 23 months ago by
Michael Love
41k • written 23 months ago by
Aurélien
• 0
1
vote
2
replies
916
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment
scater
ExperimentalDesign
scran
2.2 years ago
msn
▴ 10
1
vote
4
replies
1.3k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq
DiffBind
ExperimentalDesign
3.2 years ago • updated 3.1 years ago
SFn
• 0
6 results • Page
1 of 1
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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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