Showing : independent filtering • reset
6
votes
4
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2.6k
views
discrepance in DESeq2 results with different design structures
deseq2 differential expression independent filtering pre-filtering design matrix
9.0 years ago Assa Yeroslaviz ★ 1.5k
9
votes
6
replies
1.8k
views
Independent filtering with unequal group sizes?
independent filtering edger deseq2
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ★ 7.9k
1
vote
4
replies
1.9k
views
Selection of appropriate gene filtering method for discovering statistically significant genes for Affymetrix arrays
bioconductor differential gene expression independent filtering
9.3 years ago svlachavas ▴ 830
5
votes
4
replies
7.4k
views
edgeR cpm filter with >1 factor
edger cpm multiple factor design independent filtering
8.3 years ago dietahanson ▴ 30
18
votes
12
replies
3.7k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 8.9 years ago by 41k • written 8.9 years ago by ★ 7.9k
3
votes
13
replies
2.2k
views
Design and independent filtering of patient RNA-seq data
differential gene expression deseq2 design independent filtering limma
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 90
2
votes
3
replies
16k
views
Removing genes with very low counts in all samples before run DESeq
deseq2 statistical power independent filtering
9.4 years ago alejandro.colaneri ▴ 20
0
votes
2
replies
1.2k
views
Very high threshold for independent filtering
deseq2 mirna independent filtering
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
2
votes
3
replies
9.6k
views
Remove genes with very low counts for all samples or let DESeq2 perform independent filtering?
deseq2 independent filtering lowcountgenes
updated 8.1 years ago by 41k • written 8.1 years ago by ▴ 30
0
votes
3
replies
3.4k
views
DESeq2 independent filtering not working
deseq2 independent filtering cookscutoff
7.0 years ago tamsyn.derrick • 0
3
votes
3
replies
1.6k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
8
votes
3
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1.9k
views
Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
edgeR rnaseq limma independent filtering
6.6 years ago Robert Castelo ★ 3.3k
4
votes
11
replies
4.6k
views
edgeR cpm filter
edger independent filtering multiple factor design cpm
updated 6.5 years ago by 50k • written 6.5 years ago by • 0
0
votes
1
reply
2.8k
views
DESeq2 independent filtering using filter=rv
deseq2 INDEPENDENT FILTERING
updated 9.6 years ago by 41k • written 9.6 years ago by • 0
0
votes
6
replies
1.4k
views
contamination and DESeq2 performance
deseq2 low count genes independent filtering
updated 6.4 years ago by ▴ 20 • written 6.4 years ago by ▴ 20
0
votes
1
reply
724
views
Independent filtering very different across different contrasts
deseq2 independent filtering
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
0
votes
0
replies
1.4k
views
Specific considerations in RNA-Seq DE analysis with edgeR pipeline for a TCGA dataset starting with HTSeq counts
edgeR rnaseq DEanalysis TCGA independent filtering
6.4 years ago svlachavas ▴ 830
17 results • Page 1 of 1
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
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…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
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)
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