Showing : filtering • reset
0
votes
2
replies
310
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
8 weeks ago gingergeiger22 • 0
0
votes
1
reply
619
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
11
replies
1.9k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 20 months ago by 52k • written 20 months ago by • 0
5
votes
7
replies
1.7k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 21 months ago by 52k • written 21 months ago by ▴ 10
5
votes
8
replies
2.5k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
2.4 years ago • updated 2.3 years ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
697
views
Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
2.5 years ago Fatemeh • 0
3
votes
5
replies
2.7k
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 4.9 years ago by 43k • written 4.9 years ago by ▴ 840
0
votes
0
replies
1.3k
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
5.1 years ago jam526 • 0
2
votes
4
replies
2.4k
views
Filtering, minimum sample number, and condition in edgeR
edger filtering
updated 6.3 years ago by ★ 7.9k • written 6.3 years ago by ▴ 30
0
votes
1
reply
1.1k
views
How to keep the genes whose counts are equal or greater than 10
deseq2 filtering
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
1
vote
1
reply
1.1k
views
DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
vote
2
replies
1.3k
views
Filtering Rna-seq counts
rna-seq filtering
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 20
5
votes
12
replies
8.1k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 120
4
votes
8
replies
1.8k
views
edgeR error when trying to filter peaks with low read counts
edger R filtering
6.9 years ago camerond • 0
0
votes
2
replies
1.5k
views
Filtering genes with a minimum number of counts between samples
DESeq2 filtering
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 40
1
vote
1
reply
2.1k
views
Filtering a BED file according to genomic annotation
bed files bedtools filtering chipseq
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 60
0
votes
2
replies
2.0k
views
DiffBind remove low count intervals for differential analysis
diffbind filtering
7.2 years ago gasta88 • 0
0
votes
2
replies
1.3k
views
DiffBind dba.report inconsistent output when using filter parameters
diffbind dba.report filtering
7.3 years ago konstantopoulos • 0
1
vote
3
replies
5.9k
views
DESeq2: How to manually perform filtering and outlier detection?
deseq2 filtering outliers count outliers
updated 7.6 years ago by ★ 13k • written 7.6 years ago by ▴ 10
1
vote
6
replies
2.2k
views
Nonspecific filtering of microarray data
microarray affymetrix microarrays pre-filtering filtering nonspecific filtering
updated 7.8 years ago by ★ 13k • written 7.8 years ago by • 0
2
votes
2
replies
1.2k
views
Limma filtering based on treatment group
limma filtering
updated 7.8 years ago by ★ 13k • written 7.8 years ago by ▴ 60
3
votes
4
replies
1.6k
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
8.4 years ago Jurat Shahidin ▴ 80
1
vote
2
replies
2.3k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger filtering cpm
updated 8.5 years ago by 52k • written 8.5 years ago by • 0
6
votes
4
replies
2.1k
views
Filtering after a contrast
deseq2 r filtering bioconductor
updated 8.6 years ago by ★ 13k • written 8.6 years ago by • 0
0
votes
1
reply
1.2k
views
Does the normalization pipeline for scran include filtering out genes with low counts?
filtering scran
updated 8.6 years ago by ★ 28k • written 8.6 years ago by • 0
9
votes
11
replies
10k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
updated 8.7 years ago by ▴ 20 • written 8.8 years ago by ▴ 20
5
votes
12
replies
2.4k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 8.9 years ago by ★ 7.9k • written 9.0 years ago by ▴ 20
2
votes
4
replies
2.5k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix limma filtering
updated 9.8 years ago by 68k • written 9.8 years ago by • 0
2
votes
7
replies
3.0k
views
Different filters with edgeR
edger filtering
9.9 years ago cpcantalapiedra • 0
3
votes
10
replies
2.7k
views
Question about converting rownames of an expression dataset to their corresponding gene symbols
filtering bioconductor genesymbols expressionset
10.0 years ago svlachavas ▴ 840
30 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
Awards • All
Popular Question to svlachavas ▴ 840
Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.1k
Popular Question to Marco • 0
Locations • All
Germany/Heidelberg/German Cancer Research Center, 16 minutes ago
United States, 17 minutes ago
USA, 43 minutes ago
Pittsburgh, United States, 1 hour ago
United States, 1 hour ago
Traffic: 1416 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6