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1.5k
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Problem with limma for two-color factorial design - Coefficients not estimable
Microarray
Normalization
limma
ArrayExpress
Microarray
Normalization
limma
ArrayExpress
14.3 years ago
Stephen Turner
▴ 290
0
votes
1
reply
938
views
annotation db for miRNA_2 Array
Annotation
Annotation
updated 14.3 years ago by
Jan Van der Goten
▴ 10 • written 14.3 years ago by
attia fatima
▴ 10
0
votes
0
replies
1.6k
views
feature filter for GENE Chip miRNA 2.0 array
Annotation
affy
Annotation
affy
14.3 years ago
Guest User
★ 13k
0
votes
0
replies
1.1k
views
annotation dbi for miRNA 2.0 Array
miRNA
Annotation
miRNA
Annotation
14.3 years ago
Guest User
★ 13k
0
votes
0
replies
1.2k
views
Regression analysis using expression microarray to determine phenotypic correlation
Microarray
Regression
Microarray
Regression
14.3 years ago
Ruppert Valentino
▴ 270
0
votes
0
replies
1.2k
views
annotation package for Schizosacharomyces pombe
Annotation
Yeast
yeast2
Annotation
Yeast
yeast2
14.3 years ago
Clémentine Dressaire
▴ 120
0
votes
4
replies
2.5k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
limma
Category
edgeR
limma
Category
edgeR
updated 14.3 years ago by
Emanuel Heitlinger
▴ 30 • written 14.3 years ago by
Gordon Smyth
53k
1
vote
12
replies
3.0k
views
Illumina array analysis
Microarray
Normalization
limma
Microarray
Normalization
limma
updated 14.3 years ago by
Wei Shi
★ 3.6k • written 14.3 years ago by
Chintanu
▴ 310
0
votes
2
replies
2.7k
views
Importing .cdt files generated by Cluster3.0 into R
updated 14.3 years ago by
Valerie Obenchain
★ 6.8k • written 14.3 years ago by
Guest User
★ 13k
0
votes
2
replies
1.9k
views
DNase Seq Analysis using R
updated 14.3 years ago by
Sean Davis
21k • written 14.3 years ago by
Samarjeet
▴ 20
1
vote
3
replies
12k
views
heatmap.2 Z-score vs logFC
updated 14.3 years ago by
Sean Davis
21k • written 14.3 years ago by
Neel Aluru
▴ 460
0
votes
0
replies
1.3k
views
Postdoctoral position in biostatistics/bioinformatics/computational biology
Sequencing
Microarray
Sequencing
Microarray
14.3 years ago
Medvedovic, Mario medvedm
▴ 20
0
votes
0
replies
815
views
how to define a forward or reverse read file
14.3 years ago
wang peter
★ 2.0k
0
votes
1
reply
1.2k
views
perWindow chr coordinates (girafe)
Annotation
girafe
Annotation
girafe
updated 14.3 years ago by
Joern Toedling
▴ 50 • written 14.3 years ago by
karlerhard@berkeley.edu
▴ 60
0
votes
1
reply
1.9k
views
GEOquery and Limma
limma
GEOquery
limma
GEOquery
updated 14.3 years ago by
Sean Davis
21k • written 14.3 years ago by
Voke AO
▴ 760
0
votes
0
replies
928
views
Statistical programmer position at FHCRC
Cancer
Cancer
14.3 years ago
Greg Finak
▴ 240
0
votes
0
replies
755
views
Boston Bioconductor Basics registration will close tomorrow.
14.3 years ago
Vincent J. Carey, Jr.
6.7k
0
votes
1
reply
1.2k
views
CDF for GeneChip miRNA 2 array
miRNA
cdf
miRNA
cdf
updated 14.3 years ago by
Guido Hooiveld
★ 4.1k • written 14.3 years ago by
Guest User
★ 13k
1
vote
1
reply
2.6k
views
two way ANOVA with limma
updated 14.3 years ago by
Gordon Smyth
53k • written 14.3 years ago by
Grant R Cramer
▴ 20
0
votes
0
replies
745
views
(no subject)
14.3 years ago
Jiuzhou song
▴ 100
0
votes
0
replies
1.5k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
Category
edgeR
Category
edgeR
14.3 years ago
Emanuel Heitlinger
▴ 30
0
votes
17
replies
3.2k
views
Coverage by base
Coverage
Coverage
14.3 years ago
rohan bareja
▴ 200
0
votes
0
replies
805
views
Sample Grouping
lumi
lumi
14.3 years ago
rajasereddy
▴ 10
0
votes
4
replies
1.6k
views
R/Bioconductor CDF to Affymetrix CDF
cdf
convert
cdf
convert
updated 14.3 years ago by
Benjamin Otto
▴ 10 • written 14.3 years ago by
Benjamin Otto
▴ 830
0
votes
4
replies
2.0k
views
edgeR design matrix
PROcess
edgeR
PROcess
edgeR
updated 14.3 years ago by
Gordon Smyth
53k • written 14.3 years ago by
lpascual
▴ 50
0
votes
1
reply
1.0k
views
question about affymetrix array:ht-hg-u133acdf
Microarray
cdf
Microarray
cdf
updated 14.3 years ago by
James W. MacDonald
68k • written 14.3 years ago by
Guest User
★ 13k
0
votes
0
replies
1.6k
views
Postdoctoral Position in Statistical Genomics - Zurich
ASSET
ASSET
14.3 years ago
Mark Robinson
▴ 880
0
votes
1
reply
1.6k
views
RNA-Seq : comparison cuffdiff, edgeR, Partek
edgeR
edgeR
updated 14.3 years ago by
vasu punj
▴ 80 • written 14.3 years ago by
Lana Schaffer
★ 1.3k
1
vote
1
reply
2.6k
views
Problem with a specific GEO dataset.
GEOquery
GEOquery
updated 14.3 years ago by
Sean Davis
21k • written 14.3 years ago by
Guest User
★ 13k
0
votes
1
reply
1.2k
views
Regarding subread vignette
Sequencing
Alignment
Rsubread
Sequencing
Alignment
Rsubread
14.3 years ago
Wei Shi
★ 3.6k
1
vote
2
replies
2.1k
views
Limma model parameters design, combining a paired with a factorial design
limma
limma
updated 14.3 years ago by
James W. MacDonald
68k • written 14.3 years ago by
john herbert
▴ 560
0
votes
3
replies
2.6k
views
postForm in RCurl
14.3 years ago
Voke AO
▴ 760
0
votes
1
reply
1.5k
views
EdgeR: Log FC does not changes when I swap the groups
edgeR
edgeR
updated 14.3 years ago by
Gordon Smyth
53k • written 14.3 years ago by
Guest User
★ 13k
0
votes
0
replies
1.1k
views
best annotation package for drosophila (agilent gene expression)?
Annotation
Agi4x44PreProcess
Annotation
Agi4x44PreProcess
14.3 years ago
Jarek Bryk
▴ 110
0
votes
2
replies
2.3k
views
Is it possible to generate an ExpressionSet object that contain duplicate row names?
Annotation
Annotation
updated 14.3 years ago by
Tim Triche
★ 4.2k • written 14.3 years ago by
nqueralt@clinic.ub.es
▴ 60
0
votes
0
replies
1.2k
views
a question about getCdfInfo package in GCRMA, thanks for your help.
Annotation
cdf
makecdfenv
Annotation
cdf
makecdfenv
14.3 years ago
boczniak767
▴ 740
0
votes
0
replies
873
views
BSgenome package for sacCer3
Cancer
BSgenome
BSgenome
Cancer
BSgenome
BSgenome
14.3 years ago
Hervé Pagès
16k
0
votes
0
replies
849
views
Why are there different number of pathways in pathway2gene and in pathway2name (KEGG.db)?
Pathways
Pathways
14.3 years ago
Peng Yu
▴ 950
0
votes
5
replies
1.7k
views
need help with SNP6.0 quantile normalization
SNP
Normalization
cdf
SNP
Normalization
cdf
updated 14.3 years ago by
Vincent J. Carey, Jr.
6.7k • written 14.3 years ago by
qian liu
▴ 30
0
votes
0
replies
1.5k
views
[Job] Functional genomic analysis of cancer/RNAi screening
Transcription
Sequencing
Genetics
Pathways
Cancer
Prostate
Transcription
Sequencing
Cancer
14.3 years ago
Sean Davis
21k
0
votes
1
reply
2.0k
views
read.maimage error message
updated 14.3 years ago by
boczniak767
▴ 740 • written 14.3 years ago by
Guest User
★ 13k
0
votes
2
replies
2.6k
views
Installing packages on R v2.13.2, OSX multiple warning messages
Annotation
cdf
probe
affy
gcrma
Annotation
cdf
probe
affy
gcrma
updated 14.3 years ago by
James W. MacDonald
68k • written 14.3 years ago by
Guest User
★ 13k
0
votes
0
replies
968
views
ChIPpeakAnno - for genes with multiple isoforms
Transcription
Annotation
annotate
ChIPpeakAnno
Transcription
Annotation
annotate
14.3 years ago
Julie Zhu
★ 4.3k
0
votes
0
replies
1.1k
views
Fwd: Problems with edgeR for differential expression
Normalization
limma
edgeR
DESeq
Normalization
limma
edgeR
DESeq
14.3 years ago
Nick Schurch
▴ 60
0
votes
4
replies
1.9k
views
Problems with edgeR for differential expression
Normalization
edgeR
Normalization
edgeR
updated 14.3 years ago by
Nick Schurch
▴ 60 • written 14.3 years ago by
Gordon Smyth
53k
0
votes
1
reply
925
views
report a problem
updated 14.3 years ago by
Harris A. Jaffee
▴ 590 • written 14.3 years ago by
wang peter
★ 2.0k
0
votes
1
reply
924
views
still the trimLRPatterns problem
updated 14.3 years ago by
Harris A. Jaffee
▴ 590 • written 14.3 years ago by
wang peter
★ 2.0k
0
votes
0
replies
1.6k
views
Bioinformatics course - October 2011 Registration is now open
Microarray
Cancer
biomaRt
ArrayExpress
genomes
SANTA
Microarray
Cancer
biomaRt
genomes
14.3 years ago
Claude Chelala
▴ 40
0
votes
2
replies
1.9k
views
Weird error when installing VariantAnnotation and/or snpStats (whether from SVN or using biocLite)
snpStats
snpStats
updated 14.3 years ago by
Martin Morgan
25k • written 14.3 years ago by
Tim Triche
★ 4.2k
0
votes
8
replies
4.5k
views
Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts
updated 14.3 years ago by
Wei Shi
★ 3.6k • written 14.3 years ago by
Tim Triche
★ 4.2k
46,732 results • Page
615 of 935
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Answer: lfc shrinkage estimator in DESeq2
by
plumsgorillas
• 0
You are on the right track. In DESeq2, raw log2 fold changes are often noisy and can be misleading, especially for genes with low counts. A…
Answer: Array weights in dpcDE
by
Gordon Smyth
53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. However,…
Answer: lfc shrinkage estimator in DESeq2
by
Michael Love
43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice
by
Gordon Smyth
53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice
by
SamGG
▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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