Showing : Filtering • reset
3
votes
11
replies
1.3k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 9 months ago by 50k • written 10 months ago by • 0
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 10 months ago by 50k • written 10 months ago by ▴ 10
5
votes
8
replies
1.8k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
19 months ago • updated 16 months ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
491
views
Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
20 months ago Fatemeh • 0
3
votes
5
replies
2.1k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 4.0 years ago by 41k • written 4.0 years ago by ▴ 830
0
votes
0
replies
968
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
4.2 years ago jam526 • 0
2
votes
4
replies
1.7k
views
Filtering, minimum sample number, and condition in edgeR
edger filtering
updated 5.4 years ago by ★ 7.9k • written 5.4 years ago by ▴ 20
0
votes
1
reply
699
views
How to keep the genes whose counts are equal or greater than 10
deseq2 filtering
updated 5.4 years ago by 65k • written 5.4 years ago by • 0
1
vote
1
reply
824
views
DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
1
vote
2
replies
1.1k
views
Filtering Rna-seq counts
rna-seq filtering
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 20
5
votes
12
replies
6.4k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 110
4
votes
8
replies
1.5k
views
edgeR error when trying to filter peaks with low read counts
edger R filtering
6.0 years ago camerond • 0
0
votes
2
replies
1.2k
views
Filtering genes with a minimum number of counts between samples
DESeq2 filtering
updated 6.2 years ago by 41k • written 6.2 years ago by ▴ 40
1
vote
1
reply
1.5k
views
Filtering a BED file according to genomic annotation
bed files bedtools filtering chipseq
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 60
0
votes
2
replies
1.7k
views
DiffBind remove low count intervals for differential analysis
diffbind filtering
6.4 years ago gasta88 • 0
0
votes
2
replies
1.0k
views
DiffBind dba.report inconsistent output when using filter parameters
diffbind dba.report filtering
6.4 years ago konstantopoulos • 0
1
vote
3
replies
5.1k
views
DESeq2: How to manually perform filtering and outlier detection?
deseq2 filtering outliers count outliers
updated 6.7 years ago by ★ 13k • written 6.7 years ago by ▴ 10
1
vote
6
replies
1.9k
views
Nonspecific filtering of microarray data
microarray affymetrix microarrays pre-filtering filtering nonspecific filtering
updated 6.9 years ago by ★ 13k • written 6.9 years ago by • 0
2
votes
2
replies
1.0k
views
Limma filtering based on treatment group
limma filtering
updated 6.9 years ago by ★ 13k • written 6.9 years ago by ▴ 60
3
votes
4
replies
1.3k
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
7.6 years ago Jurat Shahidin ▴ 80
1
vote
2
replies
2.0k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger filtering cpm
updated 7.6 years ago by 50k • written 7.6 years ago by • 0
6
votes
4
replies
1.7k
views
Filtering after a contrast
deseq2 r filtering bioconductor
updated 7.7 years ago by ★ 13k • written 7.7 years ago by • 0
0
votes
1
reply
1.0k
views
Does the normalization pipeline for scran include filtering out genes with low counts?
filtering scran
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
8
votes
11
replies
9.3k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
updated 7.8 years ago by ▴ 20 • written 7.9 years ago by ▴ 10
5
votes
12
replies
1.9k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 8.1 years ago by ★ 7.9k • written 8.1 years ago by ▴ 20
2
votes
4
replies
2.1k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix limma filtering
updated 9.0 years ago by 65k • written 9.0 years ago by • 0
2
votes
7
replies
2.7k
views
Different filters with edgeR
edger filtering
9.1 years ago cpcantalapiedra • 0
3
votes
10
replies
2.3k
views
Question about converting rownames of an expression dataset to their corresponding gene symbols
filtering bioconductor genesymbols expressionset
9.1 years ago svlachavas ▴ 830
28 results • Page 1 of 1
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Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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