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1. comparing chip Information in meta analysis / Rankprod and 2. two color normalization
RankProd
RankProd
11.7 years ago
Stefanie Busch
▴ 30
2
votes
30
replies
6.1k
views
ggbio 1.12.0 autoplot() with txdb example is broken
TranscriptDb
TranscriptDb
updated 11.7 years ago by
Tengfei Yin
▴ 490 • written 11.8 years ago by
Leonardo Collado Torres
★ 1.1k
0
votes
2
replies
2.1k
views
RGraphiz installation keeps on failing ubuntu 12.04 LTS server
Rgraphviz
Rgraphviz
updated 11.7 years ago by
Frederiek - Maarten Kerckhof
▴ 10 • written 11.7 years ago by
Guest User
★ 13k
0
votes
0
replies
812
views
RGraphiz installation keeps on failing ubuntu 12.04 LTS server
11.7 years ago
Kasper Hansen
▴ 30
0
votes
1
reply
2.2k
views
how to set up sampleInfo for methylation array in illumina 450K
lumi
lumi
updated 11.7 years ago by
Pan Du
▴ 440 • written 11.7 years ago by
Guest User
★ 13k
0
votes
0
replies
1.4k
views
Insignificant q-values in minfi
minfi
minfi
11.7 years ago
Guest User
★ 13k
0
votes
0
replies
1.9k
views
Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
Sequencing
Epigenetics
PROcess
Sequencing
Epigenetics
PROcess
11.7 years ago
Brian Herb
▴ 80
0
votes
2
replies
1.0k
views
limma small vs large number of samples
updated 11.7 years ago by
James W. MacDonald
68k • written 11.7 years ago by
Giovanni Bucci
▴ 60
0
votes
0
replies
908
views
Strange error using the \"narrow\" function for a ShortReadQ object
11.7 years ago
Guest User
★ 13k
0
votes
0
replies
1.7k
views
GEOquery/virtualArray package error
Preprocessing
hgu95av2
virtualArray
Preprocessing
hgu95av2
virtualArray
11.7 years ago
Guest User
★ 13k
0
votes
4
replies
3.3k
views
EdgeR: dispersion estimation
edgeR
edgeR
11.8 years ago • updated 11.7 years ago
Guest User
★ 13k
0
votes
0
replies
829
views
package for iAUC determination using gene expression data?
11.7 years ago
Guido Hooiveld
★ 4.1k
0
votes
1
reply
784
views
error when using waveTiling package
updated 11.7 years ago by
James W. MacDonald
68k • written 11.7 years ago by
chris blazier
▴ 10
2
votes
1
reply
2.1k
views
Rgraphviz install problem.HELP!!!!!
Rgraphviz
Rgraphviz
updated 11.7 years ago by
Kasper Hansen
▴ 30 • written 11.8 years ago by
Guest User
★ 13k
0
votes
0
replies
1.1k
views
Unknown failure in virtualArrayLoadRaw
virtualArray
virtualArray
11.7 years ago
Guest User
★ 13k
0
votes
0
replies
1.5k
views
答复: 答复: 答复: problem with \"readCufflinks\"
cummeRbund
BiocGenerics
cummeRbund
BiocGenerics
11.8 years ago
Dan Tenenbaum
★ 8.2k
0
votes
0
replies
904
views
Genes Symbols lists question
minfi
minfi
11.8 years ago
Giovanni Calice
▴ 160
0
votes
0
replies
2.2k
views
hclust and cutree
11.8 years ago
chris Jhon
▴ 260
0
votes
0
replies
3.8k
views
ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0
Normalization
Clustering
affy
Normalization
Clustering
affy
11.8 years ago
Guan
▴ 20
1
vote
6
replies
2.7k
views
edgeR - paired samples with multifactorial design - errors
RNASeq
RNASeq
updated 11.8 years ago by
Devon Ryan
▴ 200 • written 11.8 years ago by
Guest User
★ 13k
0
votes
0
replies
1.8k
views
Draft support for HTA 2.0 with oligo
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
11.8 years ago
Elena Serrano
▴ 30
1
vote
12
replies
6.0k
views
EdgeR: replicated pools, yes or not?
RNASeq
Microarray
edgeR
RNASeq
Microarray
edgeR
updated 11.8 years ago by
Ryan C. Thompson
★ 7.9k • written 11.8 years ago by
Guest User
★ 13k
0
votes
2
replies
2.0k
views
DESeq2 16S copy number correction
DESeq2
DESeq2
updated 11.8 years ago by
Susan Holmes
▴ 10 • written 11.8 years ago by
Manoeli Lupatini
▴ 10
0
votes
0
replies
926
views
dmpFinder Gene ID question
11.8 years ago
Giovanni Calice
▴ 160
0
votes
0
replies
1.7k
views
Plotting per base coverage from genomecoveragebed utility
graph
graph
11.8 years ago
gv
▴ 30
0
votes
3
replies
4.4k
views
unknown error in DiffBind package
ChIPSeq
chipseq
DiffBind
ChIPSeq
chipseq
DiffBind
updated 11.8 years ago by
Rory Stark
★ 5.2k • written 11.8 years ago by
Guest User
★ 13k
0
votes
1
reply
1.0k
views
Unsubscribe me from list
updated 11.8 years ago by
Dan Tenenbaum
★ 8.2k • written 11.8 years ago by
Abugri James
▴ 20
0
votes
0
replies
2.5k
views
Pathview question
Network
convert
pathview
Network
convert
pathview
11.8 years ago
Luo Weijun
★ 1.6k
0
votes
9
replies
3.2k
views
ReportingTools gene IDs
convert
convert
updated 11.8 years ago by
James W. MacDonald
68k • written 11.8 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
1.4k
views
答复: 答复: problem with \"readCufflinks\"
cummeRbund
cummeRbund
updated 11.8 years ago by
Peng.Zhou@csiro.au
▴ 20 • written 11.8 years ago by
Dan Tenenbaum
★ 8.2k
0
votes
0
replies
1.1k
views
dmpFinder method question
minfi
minfi
11.8 years ago
Giovanni Calice
▴ 160
2
votes
19
replies
3.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome
DESeq
Microbiome
DESeq
updated 11.8 years ago by
Michael Love
43k • written 11.8 years ago by
Sophie Josephine Weiss
▴ 130
0
votes
0
replies
2.6k
views
Affymetrix HTA 2 array analysis
BiocViews
Annotation
Cancer
Breast
Organism
PROcess
biocViews
pdInfoBuilder
BiocViews
11.8 years ago
Elena Serrano
▴ 30
0
votes
1
reply
2.0k
views
ChIPpeakAnno
annotate
ChIPpeakAnno
annotate
ChIPpeakAnno
updated 11.8 years ago by
Julie Zhu
★ 4.3k • written 11.8 years ago by
Paolo Kunderfranco
▴ 350
0
votes
5
replies
2.0k
views
Comparison of murine and human microarray data
Microarray
Normalization
affy
Microarray
Normalization
affy
updated 11.8 years ago by
Stephen Piccolo
▴ 600 • written 11.8 years ago by
Bas van Gestel
▴ 20
1
vote
3
replies
4.8k
views
Blast analysis of two sequences in R
Coverage
Coverage
updated 11.8 years ago by
Martin Morgan
25k • written 11.8 years ago by
prabhakar ghorpade
▴ 100
0
votes
1
reply
1.0k
views
summarizeOverlaps: number of dropped reads
updated 11.8 years ago by
Valerie Obenchain
★ 6.8k • written 11.8 years ago by
Gabriele Schweikert
▴ 10
0
votes
3
replies
2.0k
views
MLSeq Mathematical Concepts
Classification
edgeR
DESeq
MLSeq
Classification
edgeR
DESeq
MLSeq
updated 11.8 years ago by
Wolfgang Huber
★ 13k • written 11.8 years ago by
Dario Strbenac
★ 1.6k
0
votes
3
replies
2.1k
views
Elephant shark genome
Biostrings
genomes
Biostrings
genomes
updated 11.8 years ago by
Martin Morgan
25k • written 11.8 years ago by
Guest User
★ 13k
0
votes
0
replies
784
views
Testing sensitivity and specificity on random biological sequence
11.8 years ago
Jiří Hon
▴ 20
0
votes
2
replies
1.7k
views
dexseq fitDispersionFunction(ecs) error
GO
DEXSeq
GO
DEXSeq
updated 11.8 years ago by
Alejandro Reyes
★ 1.9k • written 11.8 years ago by
Rao,Xiayu
▴ 550
0
votes
1
reply
3.0k
views
RNA seq
Annotation
Annotation
updated 11.8 years ago by
Aliaksei Holik
▴ 350 • written 11.8 years ago by
Guest User
★ 13k
0
votes
0
replies
855
views
normalization
Normalization
Normalization
11.8 years ago
Yashwant Kumar
▴ 10
0
votes
11
replies
3.4k
views
countOverlaps Warnings
updated 11.8 years ago by
Valerie Obenchain
★ 6.8k • written 11.8 years ago by
Pankaj Agarwal
▴ 100
0
votes
0
replies
2.0k
views
答复: problem with \"readCufflinks\"
cummeRbund
cummeRbund
11.8 years ago
Dan Tenenbaum
★ 8.2k
0
votes
3
replies
1.7k
views
The installation of XVector
updated 11.8 years ago by
Hervé Pagès
16k • written 11.8 years ago by
Guest User
★ 13k
0
votes
1
reply
2.7k
views
problem with \"readCufflinks\"
cummeRbund
cummeRbund
updated 11.8 years ago by
Dan Tenenbaum
★ 8.2k • written 11.8 years ago by
Guest User
★ 13k
0
votes
1
reply
1.1k
views
Counterintuitive results from edgeR
edgeR
edgeR
updated 11.8 years ago by
Gordon Smyth
53k • written 11.8 years ago by
Son Pham
▴ 60
0
votes
0
replies
2.0k
views
Ontology lack in goProfiles : no BP or CC just MF
GO
goProfiles
GO
goProfiles
11.8 years ago
Arnaud Mounier
▴ 40
0
votes
8
replies
2.7k
views
limma modeling, paired samples and continuous variable
updated 11.8 years ago by
Gordon Smyth
53k • written 11.8 years ago by
Guest User
★ 13k
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Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Hugo Gruson
• 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
Comment: Are individual-mouse-based statistics possible in CellChat?
by
LillianaVolkman99
• 0
thank you very much. https://www.biostars.org/p/9617271/
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
My apologies, I forgot that `design.group` is not included in the final matrix, because the baseline group effects are already captured by …
Answer: Bile acid analysis with limpa
by
Gordon Smyth
53k
I am not familiar with targeted HPLC-MS and I don't know what you mean by "peak areas". If it produces standard format mass spec data from …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
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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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