Showing : INDEPENDENT FILTERING • reset
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
9
votes
6
replies
1.8k
views
Independent filtering with unequal group sizes?
independent filtering edger deseq2
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ★ 7.9k
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
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
5
votes
4
replies
7.5k
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
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
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
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
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
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
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
3
replies
3.4k
views
DESeq2 independent filtering not working
deseq2 independent filtering cookscutoff
7.0 years ago tamsyn.derrick • 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
1
reply
726
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
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
17 results • Page 1 of 1
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Replies
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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