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1.1k
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Simpleaffy problems
Annotation
probe
affy
matchprobes
simpleaffy
AnnotationDbi
Annotation
probe
affy
15.3 years ago
James W. MacDonald
68k
0
votes
0
replies
1.5k
views
error in plotKEGGGraph
Pathways
GLAD
KEGGgraph
Pathways
GLAD
KEGGgraph
15.3 years ago
Robert M. Flight
▴ 280
0
votes
3
replies
1.3k
views
caught segfault in arrayQualityMetrics
arrayQualityMetrics
arrayQualityMetrics
updated 15.3 years ago by
Wolfgang Huber
★ 13k • written 15.3 years ago by
Laurent Gatto
1.6k
0
votes
2
replies
1.5k
views
BioMaRt query
ath1121501
annotate
ath1121501
annotate
updated 15.3 years ago by
James W. MacDonald
68k • written 15.3 years ago by
René Dreos
▴ 80
0
votes
3
replies
1.7k
views
R command readIllumina with beadarray
updated 15.3 years ago by
Matthew Ritchie
▴ 1000 • written 15.3 years ago by
Hajar Hassani Lahsinoui
▴ 120
0
votes
1
reply
1.4k
views
crlmm package and allele-specific CNV with Illumina SNP arrays
SNP
crlmm
SNP
crlmm
updated 15.3 years ago by
Rob Scharpf
▴ 250 • written 15.3 years ago by
Zoppoli, Gabriele NIH/NCI [G]
▴ 20
0
votes
4
replies
4.2k
views
Installing Bioconductor on Linux...
updated 15.3 years ago by
Martin Morgan
25k • written 15.3 years ago by
James Carman
▴ 150
0
votes
0
replies
835
views
Rif: Limma: nestedF and interaction term
15.3 years ago
MassimoAcquaviva@ospedale-gaslini.ge.it
▴ 40
0
votes
3
replies
1.7k
views
AgiMicroRna problems
miRNA
Normalization
FeatureExtraction
PROcess
microRNA
AgiMicroRna
miRNA
Normalization
updated 15.3 years ago by
Mike Walter
▴ 230 • written 15.3 years ago by
Mark Cowley
▴ 910
0
votes
2
replies
1.2k
views
Rsamtools Memory Issue
updated 15.3 years ago by
Martin Morgan
25k • written 15.3 years ago by
wrighth
▴ 260
0
votes
3
replies
4.3k
views
Unambiguously mapping of affy IDs to gene symbols using hgu133plus2.db
Annotation
hgu133plus2
biomaRt
Annotation
hgu133plus2
biomaRt
updated 15.3 years ago by
Marc Carlson
★ 7.2k • written 15.3 years ago by
Christian Ruckert
▴ 170
0
votes
2
replies
1.3k
views
RdbiPgSQL installation trouble
RdbiPgSQL
RdbiPgSQL
updated 15.3 years ago by
Martin Morgan
25k • written 15.3 years ago by
Tena Sakai
▴ 40
0
votes
1
reply
949
views
Help Handling potential siRNA off target effects
limma
limma
updated 15.3 years ago by
Wolfgang Huber
★ 13k • written 15.3 years ago by
Lloyd, Bryony
▴ 20
0
votes
0
replies
1.1k
views
Several faculty positions in Statistics and Bioinformatics at Penn State
GO
GO
15.3 years ago
Naomi Altman
★ 6.0k
0
votes
1
reply
1.2k
views
Problem with genomicFeatures: id2name
BSgenome
biomaRt
BSgenome
GenomicFeatures
BSgenome
biomaRt
BSgenome
GenomicFeatures
updated 15.3 years ago by
Marc Carlson
★ 7.2k • written 15.3 years ago by
Paul Leo
▴ 970
0
votes
1
reply
1.5k
views
Limma: nestedF and interaction term
limma
limma
updated 15.3 years ago by
James W. MacDonald
68k • written 15.3 years ago by
MassimoAcquaviva@ospedale-gaslini.ge.it
▴ 40
0
votes
0
replies
754
views
yet another gene universe question
15.3 years ago
Max Kuhn
▴ 60
0
votes
1
reply
932
views
Biostrings pdf, missing? 'Efficient genome searching with Biostrings and the BSgenome data package'
Preprocessing
BSgenome
Biostrings
BSgenome
Preprocessing
BSgenome
Biostrings
BSgenome
updated 15.3 years ago by
Dan Tenenbaum
★ 8.2k • written 15.3 years ago by
Paul Shannon
★ 1.1k
0
votes
2
replies
978
views
Illumina Methylation data
updated 15.3 years ago by
Tim Triche
★ 4.2k • written 15.3 years ago by
sisitzq@gmail.com
▴ 50
0
votes
3
replies
1.4k
views
how to save the expression values for two color data after normalization
15.3 years ago
Budhayash Gautam
▴ 90
0
votes
1
reply
1.1k
views
Bug in G/IRanges when slicing with an Rle containing only 1 runLength/value
Cancer
Cancer
updated 15.3 years ago by
Martin Morgan
25k • written 15.3 years ago by
Steve Lianoglou
★ 13k
0
votes
2
replies
1.0k
views
how to give input to geneAnswer
updated 15.3 years ago by
Steve Lianoglou
★ 13k • written 15.3 years ago by
Budhayash Gautam
▴ 90
0
votes
1
reply
1.4k
views
exonmap/xmapcore and splicing.index
exonmap
xmapcore
exonmap
xmapcore
updated 15.3 years ago by
Michal Okoniewski
▴ 190 • written 15.3 years ago by
Peter Saffrey
▴ 70
0
votes
8
replies
2.5k
views
AgiMicroRna problems
Normalization
PROcess
microRNA
AgiMicroRna
Normalization
PROcess
microRNA
AgiMicroRna
15.3 years ago
Mark Cowley
▴ 910
0
votes
14
replies
3.0k
views
reading data from Beadarray into R
beadarray
beadarray
updated 15.3 years ago by
Steve Lianoglou
★ 13k • written 15.3 years ago by
Hajar Hassani Lahsinoui
▴ 120
0
votes
0
replies
891
views
how to save the expression values for two color data after normalization
Annotation
Annotation
15.3 years ago
boczniak767
▴ 740
0
votes
1
reply
785
views
Feedback on Affymetrix background adjustment
Normalization
Normalization
updated 15.3 years ago by
James W. MacDonald
68k • written 15.3 years ago by
ANJAN PURKAYASTHA
▴ 110
0
votes
0
replies
1.4k
views
Flagging overlapping gene exons (was Re: Question about CSAMA10 ...)
Annotation
Cancer
IRanges
GenomicFeatures
GenomicRanges
Annotation
Cancer
IRanges
15.3 years ago
Steve Lianoglou
★ 13k
0
votes
4
replies
1.4k
views
Normalization questions
Normalization
Normalization
updated 15.3 years ago by
Wolfgang Huber
★ 13k • written 15.3 years ago by
ANJAN PURKAYASTHA
▴ 110
0
votes
1
reply
1.1k
views
Simpleaffy problems
affy
affy
updated 15.3 years ago by
James W. MacDonald
68k • written 15.3 years ago by
ANJAN PURKAYASTHA
▴ 110
0
votes
7
replies
1.7k
views
Simulation of the beta average
updated 15.3 years ago by
Sean Davis
21k • written 15.3 years ago by
Samor Gandhi
▴ 40
0
votes
1
reply
2.1k
views
Question: How does limma derives its logFC value in two colored arrays?
Yeast
affy
vsn
limma
Yeast
affy
vsn
limma
updated 15.3 years ago by
Sunny Srivastava
▴ 350 • written 15.3 years ago by
Gordon Smyth
53k
3
votes
1
reply
4.2k
views
Right skewed histogram of p-values
limma
limma
updated 15.3 years ago by
Simon Anders
★ 3.8k • written 15.3 years ago by
Giulio Di Giovanni
▴ 540
0
votes
1
reply
1.1k
views
install error in GeneRfold
BSgenome
BSgenome
GeneRfold
BSgenome
BSgenome
GeneRfold
updated 15.3 years ago by
Heidi Dvinge
★ 2.0k • written 15.3 years ago by
Yuan Jian
▴ 250
0
votes
2
replies
871
views
PM values for probes in a probeset: background corrected and normalized, but not summarized?
Normalization
affy
Normalization
affy
updated 15.3 years ago by
James W. MacDonald
68k • written 15.3 years ago by
Glazko, Galina
▴ 350
0
votes
2
replies
1.6k
views
Quantile normalization in Ringo package
Ringo
Ringo
updated 15.3 years ago by
Joern Toedling
▴ 450 • written 15.3 years ago by
Mohamed Lajnef
▴ 250
0
votes
4
replies
2.6k
views
applying p.adjust() in limma
limma
limma
updated 15.3 years ago by
Sunny Srivastava
▴ 350 • written 15.3 years ago by
Xiaokuan Wei
▴ 230
0
votes
0
replies
1.4k
views
Agi4x44PreProcess
GUI
zebrafish
probe
AgiMicroRna
GUI
zebrafish
probe
AgiMicroRna
15.3 years ago
Neel Aluru
▴ 460
0
votes
1
reply
1.4k
views
Help on extracting up-regulated genes with limma
Microarray
limma
Microarray
limma
updated 15.3 years ago by
Sean Davis
21k • written 15.3 years ago by
Victoria Hu
▴ 10
0
votes
1
reply
1.6k
views
Question about topTable
GO
GO
updated 15.3 years ago by
Mark Cowley
▴ 910 • written 15.3 years ago by
Casper Shyr
▴ 140
0
votes
0
replies
989
views
Question: How does limma derives its logFC value in two colored arrays?
affy
limma
affy
limma
15.3 years ago
Sunny Srivastava
▴ 350
0
votes
1
reply
1.2k
views
PlateCore questions
plateCore
plateCore
updated 15.3 years ago by
Errol Strain
▴ 40 • written 15.3 years ago by
Sancho, Jose
▴ 80
0
votes
0
replies
1.2k
views
unbalanced block design using limma
affy
limma
affy
limma
15.3 years ago
Gordon Smyth
53k
0
votes
0
replies
1.1k
views
goTools question
probe
goTools
probe
goTools
15.3 years ago
Pete Shepard
▴ 240
0
votes
0
replies
2.1k
views
BioNet - interpretation of node score (Eva Benito Garagorri)
SNP
Microarray
GO
Network
Clustering
Cancer
Organism
mgug4122a
probe
limma
convert
SNP
15.3 years ago
Daniela Beißer
▴ 20
0
votes
3
replies
1.1k
views
Puzzled about limma and PAM results validity
limma
limma
15.3 years ago
Giulio Di Giovanni
▴ 540
0
votes
4
replies
1.9k
views
ShortRead for sequencing data quality assessment
Sequencing
ShortRead
Sequencing
ShortRead
15.3 years ago
heyi xiao
▴ 360
0
votes
2
replies
1.1k
views
snpMatrix: read.plink() allocMatrix: too many elements specified
updated 15.3 years ago by
Benilton Carvalho
★ 4.3k • written 15.3 years ago by
Jim Moon
▴ 10
0
votes
5
replies
1.6k
views
Package "xps" "import.expr.scheme" problem
Annotation
cdf
probe
Annotation
cdf
probe
updated 15.3 years ago by
cstrato
★ 3.9k • written 15.3 years ago by
Naïma Oumouhou
▴ 80
0
votes
0
replies
1.3k
views
unbalanced block design using limma
affy
limma
affy
limma
15.3 years ago
julin@aecom.yu.edu
▴ 80
46,719 results • Page
656 of 935
Recent ...
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Comment: Development of MSstat workflow to analyze DIA time series data
by
Gordon Smyth
53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR
by
Gordon Smyth
53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Comment: Clarification on counting in Rsubread (featureCounts)
by
Gordon Smyth
53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package
by
Nguyen
• 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
James W. MacDonald
68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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