Showing : genefilter • reset
6
votes
5
replies
14k
views
Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 10
10
votes
23
replies
13k
views
Macbook M1 install genefilter failed
DESeq2 m1 macbook genefilter
2.7 years ago • updated 17 months ago soda ▴ 80
1
vote
3
replies
9.0k
views
genefilter installation error
genefilter genefilter
updated 9.7 years ago by ▴ 150 • written 9.7 years ago by ▴ 10
0
votes
1
reply
3.9k
views
error in installing \"genefilter\"
genefilter genefilter
updated 10.0 years ago by 65k • written 10.0 years ago by ★ 13k
0
votes
6
replies
3.3k
views
how to convert a AffyBatch into ExpressionSet object ?
Annotation GO Survival ExperimentData cdf DynDoc genefilter geneplotter multtest affy GO
updated 16.7 years ago by ▴ 220 • written 16.7 years ago by ★ 2.2k
0
votes
3
replies
3.3k
views
Installing genefilter
Microarray genefilter multtest Microarray genefilter multtest
updated 19.2 years ago by ▴ 300 • written 19.2 years ago by ▴ 20
0
votes
8
replies
3.2k
views
Reading Agilent files using read.maimages
Survival DynDoc genefilter tkWidgets affy vsn marray convert ArrayExpress Survival affy
updated 16.7 years ago by ▴ 20 • written 16.7 years ago by ▴ 100
0
votes
1
reply
3.2k
views
RE : create an new AnnotatedDataFrame
Annotation Survival Yeast Biobase genefilter tkWidgets marray convert arrayMagic affyio
updated 16.7 years ago by 25k • written 16.7 years ago by ▴ 30
0
votes
1
reply
3.0k
views
2 way anova in Bioconductor
Microarray GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics BRAIN
updated 12.8 years ago by ▴ 210 • written 12.8 years ago by ▴ 110
1
vote
3
replies
2.9k
views
DESeq2/genefilter compatibility with R 4.2.2
DESeq2 genefilter
17 months ago Morgane ▴ 10
0
votes
2
replies
2.9k
views
Error with oligo: environmentIsLocked
oligo bioconductor genefilter
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 10
0
votes
2
replies
2.9k
views
Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 17.4 years ago by ★ 7.4k • written 17.4 years ago by ▴ 360
0
votes
1
reply
2.8k
views
ReadAffy can not find function read.AnnotatedDataFrame
Biobase genefilter affydata limma simpleaffy hopach affyio Biobase genefilter affydata
updated 17.4 years ago by 65k • written 17.4 years ago by ▴ 510
0
votes
11
replies
2.7k
views
trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 17.4 years ago by ▴ 10 • written 17.4 years ago by ★ 2.2k
0
votes
0
replies
2.7k
views
Error: (subscript) logical subscript too long. Help, please?
Cancer genefilter Cancer genefilter
20.8 years ago Fátima Núñez ▴ 130
0
votes
2
replies
2.7k
views
installing problem - preprocessCore, affy on linux platform
Biobase genefilter affy vsn gcrma matchprobes preprocessCore Biobase genefilter affy vsn
updated 15.6 years ago by ★ 6.5k • written 15.6 years ago by ▴ 20
4
votes
4
replies
2.6k
views
DEXSeq and Independent filtering
dexseq deseq2 genefilter
updated 8.4 years ago by ★ 13k • written 8.4 years ago by ▴ 20
4
votes
4
replies
2.6k
views
Non-specific filtering methodogies for ExpressionSet in R/Bioconductor
genefilter R bioconductor differential gene expression
updated 9.3 years ago by 50k • written 9.3 years ago by ▴ 830
0
votes
2
replies
2.4k
views
[R] Select single probe-set with median expression from multiple probe-sets corresponding to same gene -AFFY
GO probe Biobase genefilter GO probe Biobase genefilter
updated 11.1 years ago by 25k • written 11.1 years ago by ▴ 30
2
votes
12
replies
2.4k
views
I want to order genes in GO groups
gene ontology genefilter
updated 8.6 years ago by ▴ 360 • written 8.6 years ago by ▴ 10
3
votes
5
replies
2.2k
views
Fail to install "AnnotationHub"
software error annotation genefilter pd.hta.2.0
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 20
0
votes
4
replies
2.2k
views
error while loading the genefilter package [R 2.8.1. on Mac OSX 10.5.6]
genefilter genefilter
updated 15.0 years ago by ★ 1.6k • written 15.0 years ago by ▴ 390
4
votes
4
replies
2.1k
views
Suggestions for non-specific filtering criteria with limma
limma genefilter
updated 8.3 years ago by ★ 13k • written 8.4 years ago by ▴ 10
0
votes
8
replies
2.1k
views
genefiltering before or after the normalization?
Normalization genefilter Normalization genefilter
updated 15.8 years ago by ★ 2.0k • written 15.8 years ago by ▴ 340
0
votes
1
reply
2.1k
views
Can not install packages
ballgown genefilter RskittleBrewer
updated 5.5 years ago by ★ 6.5k • written 5.5 years ago by • 0
9
votes
10
replies
2.1k
views
Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
limma microarray genefilter deseq2
4.9 years ago • updated 4.8 years ago Jurat Shahidin ▴ 80
1
vote
1
reply
2.1k
views
Removing probes with low variance across samples (Infinium 450k)
probe genefilter probe genefilter
updated 12.2 years ago by ★ 4.2k • written 12.2 years ago by ▴ 400
0
votes
3
replies
2.0k
views
Situation of the legend in the plotPCA of the affycoretools library
GO Survival cdf annotate genefilter multtest affy graph limma RBGL GOstats Category GO
updated 17.6 years ago by 65k • written 17.6 years ago by ▴ 350
7
votes
5
replies
2.0k
views
Adjusted P values
limma genefilter
updated 9.5 years ago by 50k • written 9.5 years ago by ▴ 10
1
vote
1
reply
2.0k
views
Rosetta Resolver-like error-weighted ANOVAs in Bioconductor
Microarray genefilter affy Microarray genefilter affy
updated 10.1 years ago by ★ 7.9k • written 10.1 years ago by ▴ 10
0
votes
3
replies
2.0k
views
Problem installing genefilter (Ubuntu 12.04; Bioconductor v2.12)
genefilter genefilter
updated 10.7 years ago by 65k • written 10.7 years ago by ★ 13k
0
votes
4
replies
1.9k
views
installation problem
Ruuid genefilter rhdf5 multtest affy graph Rgraphviz RBGL Ruuid genefilter rhdf5 affy
updated 20.6 years ago by 6.7k • written 20.6 years ago by ▴ 30
0
votes
6
replies
1.9k
views
2 way anova in Bioconductor
GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics GO genefilter
updated 12.8 years ago by ★ 2.0k • written 12.8 years ago by ▴ 110
0
votes
12
replies
1.9k
views
Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 17.4 years ago by ★ 5.5k • written 17.4 years ago by ▴ 460
0
votes
4
replies
1.9k
views
genefilter kOverA filter by range
genefilter genefilter
updated 10.3 years ago by 65k • written 10.3 years ago by ▴ 220
0
votes
10
replies
1.9k
views
Some Genefilter questions
Normalization Survival Cancer cdf genefilter geneplotter affy affydata widgetTools gcrma
updated 17.4 years ago by ▴ 460 • written 17.4 years ago by ▴ 70
1
vote
4
replies
1.9k
views
cran check shows that genefilter is not available
genefilter
6.4 years ago jinkaixiu ▴ 10
0
votes
5
replies
1.9k
views
affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 16.8 years ago by 65k • written 16.8 years ago by ▴ 50
0
votes
6
replies
1.9k
views
ReadAffy Error: new versions causing problems?
genefilter gcrma matchprobes simpleaffy affyio genefilter gcrma matchprobes simpleaffy
updated 16.9 years ago by ▴ 20 • written 16.9 years ago by ▴ 200
0
votes
6
replies
1.9k
views
Save ExpressionSet to csv file with columns and rows headers
microarray genefilter
updated 4.9 years ago by 65k • written 4.9 years ago by ▴ 10
6
votes
6
replies
1.8k
views
genefilter filtered out 60% of the original genes?
genefilter edgeR
updated 8.0 years ago by ▴ 180 • written 8.0 years ago by ▴ 20
0
votes
3
replies
1.8k
views
Can't get RCurl...
GO Survival annotate genefilter affy graph limma GOstats biomaRt Category affycoretools
updated 17.1 years ago by 65k • written 17.1 years ago by ★ 2.2k
0
votes
3
replies
1.8k
views
How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray
Microarray Annotation Normalization GO probe genefilter affy limma oligo Microarray GO
updated 12.0 years ago by ▴ 190 • written 12.0 years ago by 65k
0
votes
5
replies
1.8k
views
Annotating Expression Set for GSVA w/ Brainarray Human Gene 1.1 ST Array CDF
bioconductor brainarray genefilter oligo
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
9
replies
1.8k
views
problem with function rma
Normalization rat2302 cdf genefilter affy simpleaffy affyQCReport affyio Normalization
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 80
0
votes
1
reply
1.8k
views
using simpleaffy incorrectly, or is there a problem with the read.affy function?
Microarray Survival Cancer genefilter affy simpleaffy affyio Microarray Survival Cancer
17.3 years ago k. brand ▴ 420
0
votes
3
replies
1.8k
views
error in filtering genes with rowVars(gexpr(bg_chrX)) >1
genefilter ballgown
updated 6.3 years ago by • 0 • written 6.7 years ago by • 0
0
votes
1
reply
1.8k
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, ?
deseq2 filter genefilter
updated 6.4 years ago by 41k • written 6.5 years ago by • 0
0
votes
0
replies
1.7k
views
how to convert a AffyBatch into ExpressionSet object ?
Annotation GO Survival ExperimentData cdf DynDoc genefilter geneplotter multtest affy GO
16.7 years ago Min Wook Kim ▴ 20
0
votes
11
replies
1.7k
views
'recursive default argument' error in GOENTREZID2GO
GO Biobase genefilter graph Category GO Biobase genefilter graph Category
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 260
50 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
United States, just now
France, 3 minutes ago
United States, 3 minutes ago
France, 7 minutes ago
Helsinki, 8 minutes ago
Traffic: 1101 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