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Outlier
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4
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5
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6.5k
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outlier detection of RNAseq samples
deseq2
rnaseq
PCA
hierarchical clustering
outlier
7.4 years ago
wd
▴ 30
1
vote
7
replies
4.6k
views
DESeq2 outlier detection not filtering
DESeq2
outlier
RNASeq
updated 9.4 years ago by
Michael Love
41k • written 9.4 years ago by
kenneth.daily
• 0
1
vote
8
replies
1.9k
views
[Outlier Gene removal] - One sample with outlier counts for some genes
RNAseq
DESeq2
outlier
counts
DE analysis
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
DcL-A
• 0
2
votes
3
replies
1.5k
views
RNAseq outlier is a critical sample
rnaseq
outlier
statistics
batch effect
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
grastalt27
• 0
1
vote
1
reply
1.3k
views
arrayQualityMetrics for outlier detection
arrayQualityMetrics
Microarray
Outlier
updated 8.5 years ago by
Wolfgang Huber
★ 13k • written 8.5 years ago by
horcsct
▴ 10
0
votes
2
replies
1.2k
views
Which genes are outliers in DESeq2?
DESeq2
RNAseq
outlier
updated 15 months ago by
ATpoint
★ 4.1k • written 15 months ago by
James
• 0
1
vote
3
replies
745
views
DE analysis outlier removal
deseq2
outlier
normalization
removal
updated 4.1 years ago by
Michael Love
41k • written 4.1 years ago by
knholm
• 0
0
votes
1
reply
443
views
Outlier removal outcome
Outlier
updated 13 months ago by
ATpoint
★ 4.1k • written 14 months ago by
sanchita.bhattacharya
• 0
8 results • Page
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Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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