Showing : independent filtering • reset
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
2
votes
3
replies
9.5k
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
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
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
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
0
votes
3
replies
3.4k
views
DESeq2 independent filtering not working
deseq2 independent filtering cookscutoff
7.0 years ago tamsyn.derrick • 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
6
votes
4
replies
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
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
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
8
votes
3
replies
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
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
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
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
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
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
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
17 results • Page 1 of 1
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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…
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…
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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