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outlier
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4
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6.6k
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outlier detection of RNAseq samples
deseq2
rnaseq
PCA
hierarchical clustering
outlier
7.5 years ago • updated 7.4 years ago
wd
▴ 30
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
3
replies
754
views
DE analysis outlier removal
deseq2
outlier
normalization
removal
updated 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
knholm
• 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
1
vote
7
replies
4.6k
views
DESeq2 outlier detection not filtering
DESeq2
outlier
RNASeq
updated 9.4 years ago by
Michael Love
42k • written 9.4 years ago by
kenneth.daily
• 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
0
votes
1
reply
448
views
Outlier removal outcome
Outlier
updated 14 months ago by
ATpoint
★ 4.1k • written 14 months ago by
sanchita.bhattacharya
• 0
8 results • Page
1 of 1
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Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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