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pre-filtering
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6
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discrepance in DESeq2 results with different design structures
deseq2
differential expression
independent filtering
pre-filtering
design matrix
8.9 years ago
Assa Yeroslaviz
★ 1.5k
5
votes
8
replies
6.6k
views
DESeq2: Applying different pre-filtering for DE and EDA/Visualization of RNASeq data
deseq2
pre-filtering
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
Zach Roe
▴ 10
1
vote
1
reply
1.9k
views
Does manual pre-filtering of the data on read counts violate the assumptions of the dispersion estimation in DESeq2?
deseq2
pre-filtering
updated 9.0 years ago by
Michael Love
41k • written 9.0 years ago by
Johannes Rainer
★ 2.0k
0
votes
2
replies
1.3k
views
Error with DEXSeqDataSet object after performing pre-filter
DEXSeq
rownames
pre-filtering
updated 8.2 years ago by
Wolfgang Huber
★ 13k • written 8.2 years ago by
arom2
• 0
1
vote
6
replies
1.8k
views
Nonspecific filtering of microarray data
microarray
affymetrix microarrays
pre-filtering
filtering
nonspecific filtering
updated 6.8 years ago by
Wolfgang Huber
★ 13k • written 6.8 years ago by
n.lu
• 0
3
votes
7
replies
4.9k
views
Pre-filtering genes counts vs normalised counts DESeq2
deseq2
pre-filtering
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
bekah
▴ 40
6 results • Page
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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