Showing : Filtering • reset
0
votes
2
replies
198
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
13 days ago • updated 11 days ago gingergeiger22 • 0
0
votes
1
reply
570
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 5 months ago by 43k • written 6 months ago by • 0
3
votes
11
replies
1.8k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 19 months ago by 52k • written 19 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 20 months ago by 52k • written 20 months ago by ▴ 10
5
votes
8
replies
2.4k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
2.3 years ago • updated 2.1 years ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
671
views
Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
2.4 years ago Fatemeh • 0
3
votes
5
replies
2.6k
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 4.8 years ago by 43k • written 4.8 years ago by ▴ 840
0
votes
0
replies
1.2k
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
5.0 years ago jam526 • 0
2
votes
4
replies
2.3k
views
Filtering, minimum sample number, and condition in edgeR
edger filtering
updated 6.1 years ago by ★ 7.9k • written 6.1 years ago by ▴ 30
0
votes
1
reply
1.0k
views
How to keep the genes whose counts are equal or greater than 10
deseq2 filtering
updated 6.2 years ago by 67k • written 6.2 years ago by • 0
1
vote
1
reply
1.0k
views
DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
2
replies
1.3k
views
Filtering Rna-seq counts
rna-seq filtering
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 20
5
votes
12
replies
7.8k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 6.7 years ago by 52k • written 6.7 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
6.8 years ago camerond • 0
0
votes
2
replies
1.4k
views
Filtering genes with a minimum number of counts between samples
DESeq2 filtering
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 40
1
vote
1
reply
2.0k
views
Filtering a BED file according to genomic annotation
bed files bedtools filtering chipseq
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 60
0
votes
2
replies
1.9k
views
DiffBind remove low count intervals for differential analysis
diffbind filtering
7.1 years ago gasta88 • 0
0
votes
2
replies
1.2k
views
DiffBind dba.report inconsistent output when using filter parameters
diffbind dba.report filtering
7.2 years ago konstantopoulos • 0
1
vote
3
replies
5.8k
views
DESeq2: How to manually perform filtering and outlier detection?
deseq2 filtering outliers count outliers
updated 7.4 years ago by ★ 13k • written 7.4 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 7.6 years ago by ★ 13k • written 7.6 years ago by • 0
2
votes
2
replies
1.2k
views
Limma filtering based on treatment group
limma filtering
updated 7.7 years ago by ★ 13k • written 7.7 years ago by ▴ 60
3
votes
4
replies
1.5k
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
8.3 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 8.4 years ago by 52k • written 8.4 years ago by • 0
6
votes
4
replies
2.0k
views
Filtering after a contrast
deseq2 r filtering bioconductor
updated 8.4 years ago by ★ 13k • written 8.4 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 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
9
votes
11
replies
10k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
updated 8.5 years ago by ▴ 20 • written 8.7 years ago by ▴ 20
5
votes
12
replies
2.3k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by ▴ 20
2
votes
4
replies
2.4k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix limma filtering
updated 9.7 years ago by 67k • written 9.7 years ago by • 0
2
votes
7
replies
2.9k
views
Different filters with edgeR
edger filtering
9.8 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
9.8 years ago svlachavas ▴ 840
30 results • Page 1 of 1
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Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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