Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
0
votes
2
replies
4.0k
views
using Blat in R
Alignment
PROcess
Alignment
PROcess
updated 15.8 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k • written 15.8 years ago by
Fahim Md
▴ 250
0
votes
0
replies
1.1k
views
Advanced R Programming for Bioinformatics, May 20-21
Cancer
Cancer
15.8 years ago
Martin Morgan
25k
0
votes
0
replies
1.3k
views
[A question on goseq package with UCSC known gene ID]
GO
goseq
GO
goseq
15.8 years ago
sunghee OH
▴ 50
0
votes
6
replies
2.1k
views
query and subject hits in findOverlaps through different space names
IRanges
IRanges
updated 15.8 years ago by
Michael Lawrence
★ 11k • written 15.8 years ago by
Robert Castelo
★ 3.4k
0
votes
1
reply
1.0k
views
normalization between different microarray
updated 15.8 years ago by
Paul Leo
▴ 970 • written 15.8 years ago by
chittabrata mal
▴ 50
0
votes
3
replies
2.4k
views
Help please: FCS binary to ascii text using bioconductor
updated 15.8 years ago by
Josef Spidlen
▴ 140 • written 15.8 years ago by
David Lyon
▴ 340
0
votes
2
replies
984
views
Recycling vars with IRanges::reflect
Cancer
IRanges
Cancer
IRanges
updated 15.8 years ago by
Patrick Aboyoun
★ 1.6k • written 15.8 years ago by
Steve Lianoglou
★ 13k
0
votes
4
replies
1.4k
views
RNA degradation plot
graph
graph
updated 15.8 years ago by
Benilton Carvalho
★ 4.3k • written 15.8 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
4
replies
2.9k
views
snow library, question on clusterExport
updated 15.8 years ago by
Pavelka, Norman
▴ 70 • written 15.8 years ago by
mattia pelizzola
▴ 200
0
votes
11
replies
2.3k
views
Problems in MAplot for affybatch objects
updated 15.8 years ago by
Ben Bolstad
★ 1.2k • written 15.8 years ago by
Javier Pérez Florido
▴ 840
0
votes
8
replies
3.0k
views
'SRAdb useful for visualizing BAM files'
SRAdb
SRAdb
updated 15.8 years ago by
Jack Zhu
▴ 170 • written 15.8 years ago by
Paul Shannon
★ 1.1k
1
vote
1
reply
5.5k
views
edgeR: pseudocounts, logConc and logFC
Proteomics
graph
edgeR
Proteomics
graph
edgeR
updated 15.8 years ago by
Mark Robinson
★ 1.1k • written 15.8 years ago by
Ann Hess
▴ 340
0
votes
1
reply
1.0k
views
installation of Rgraphviz
Rgraphviz
Rgraphviz
updated 15.8 years ago by
Kasper Daniel Hansen
★ 6.5k • written 15.8 years ago by
Yanwei Tan
▴ 10
0
votes
1
reply
1.2k
views
Interpretation of genotype calls from Oligo crlmm algorithm
SNP
oligo
crlmm
SNP
oligo
crlmm
updated 15.8 years ago by
Benilton Carvalho
★ 4.3k • written 15.8 years ago by
jeremy wilson
▴ 150
0
votes
2
replies
871
views
Query regarding AffylmGUI
15.8 years ago
varpal singh
▴ 120
0
votes
1
reply
916
views
Problems finding a matching R annotation file...
Annotation
Annotation
updated 15.8 years ago by
Marc Carlson
★ 7.2k • written 15.8 years ago by
Nick Schurch
▴ 60
0
votes
8
replies
2.2k
views
Error GO.db package "term is not member of any ontology"
GO
GO
updated 15.8 years ago by
Sean Davis
21k • written 15.8 years ago by
Ana Conesa
▴ 340
0
votes
0
replies
982
views
p values of time serie data with timecourse package?
Microarray
GO
Microarray
GO
15.8 years ago
Helen Zhou
▴ 150
0
votes
1
reply
1.2k
views
rtracklayer 1.6: invalid class "ucscCart" object
hgu133plus2
rtracklayer
hgu133plus2
rtracklayer
updated 15.8 years ago by
Michael Lawrence
★ 11k • written 15.8 years ago by
Paul Shannon
★ 1.1k
0
votes
2
replies
1.2k
views
error in import.exon.scheme, XPS package
xps
xps
updated 15.8 years ago by
cstrato
★ 3.9k • written 15.8 years ago by
Lisa Mu
▴ 10
0
votes
1
reply
2.1k
views
pvclust and distance matrices
Clustering
Clustering
15.8 years ago
Glazko, Galina
▴ 350
0
votes
1
reply
2.5k
views
CDF environment missing for HuGene-1_0-st-v1
cdf
cdf
updated 15.8 years ago by
James W. MacDonald
68k • written 15.8 years ago by
Legaie, Roxane
▴ 20
0
votes
1
reply
1.2k
views
Query regarding GEO Database
ArrayExpress
ArrayExpress
updated 15.8 years ago by
Sean Davis
21k • written 15.8 years ago by
varpal singh
▴ 120
0
votes
6
replies
2.0k
views
load failed for 'Rlibstree'
hgu133plus2
rtracklayer
hgu133plus2
rtracklayer
updated 15.8 years ago by
Seth Falcon
★ 7.4k • written 15.8 years ago by
Paul Shannon
★ 1.1k
0
votes
1
reply
4.7k
views
Mapping onto KO numbers (KEGG Orthology)
updated 15.8 years ago by
James W. MacDonald
68k • written 15.8 years ago by
Alla Bulashevska
▴ 60
0
votes
2
replies
1.7k
views
memory allocation problem not solved
updated 15.8 years ago by
Sean Davis
21k • written 15.8 years ago by
sneha patil
▴ 220
0
votes
8
replies
2.7k
views
pdInfoBuilder: invalid class object ("ScalarCharacter")
Annotation
oligo
pdInfoBuilder
Annotation
oligo
pdInfoBuilder
updated 15.8 years ago by
Vincent J. Carey, Jr.
6.7k • written 15.8 years ago by
Guido Hooiveld
★ 4.1k
0
votes
2
replies
1.1k
views
BioC packages for Human Gene 1.0 ST arrays
updated 15.8 years ago by
Groot, Philip de
▴ 630 • written 15.8 years ago by
jiayu wen
▴ 60
0
votes
2
replies
1.2k
views
how to find the probe set ID using different CDF file?
cdf
probe
affy
cdf
probe
affy
updated 15.8 years ago by
Groot, Philip de
▴ 630 • written 15.8 years ago by
James Anderson
▴ 820
0
votes
6
replies
3.4k
views
Error in GO.db
GO
GO
updated 15.8 years ago by
Vincent J. Carey, Jr.
6.7k • written 15.8 years ago by
Mayte Suarez-Farinas
▴ 510
0
votes
6
replies
3.1k
views
consensusString Function
updated 15.8 years ago by
Patrick Aboyoun
★ 1.6k • written 15.8 years ago by
Erik Wright
▴ 210
0
votes
1
reply
1.1k
views
Query regarding memory allocation
updated 15.8 years ago by
Sean Davis
21k • written 15.8 years ago by
sneha patil
▴ 220
0
votes
0
replies
514
views
how to handle multiprobes for one gene in illumina microarray
15.8 years ago
Hai-Ri Li
▴ 20
0
votes
7
replies
1.9k
views
CGH analysis without genome positions
CGH
CGH
updated 15.8 years ago by
Sean Davis
21k • written 15.8 years ago by
adam_pgsql
▴ 70
0
votes
1
reply
834
views
Query
cdf
probe
cdf
probe
updated 15.8 years ago by
James W. MacDonald
68k • written 15.8 years ago by
sneha patil
▴ 220
0
votes
2
replies
1.0k
views
Query regarding Bioconductor package
Microarray
Microarray
updated 15.8 years ago by
Sean Davis
21k • written 15.8 years ago by
varpal singh
▴ 120
0
votes
2
replies
1.4k
views
Methylation data
updated 15.8 years ago by
Prashantha Hebbar
▴ 260 • written 15.8 years ago by
Mohamed Lajnef
▴ 250
0
votes
9
replies
2.5k
views
Error with unique
Biostrings
Biostrings
updated 15.8 years ago by
Sean Davis
21k • written 15.8 years ago by
Erik Wright
▴ 210
0
votes
6
replies
3.6k
views
converting position from '-' strand to '+' strand
convert
convert
updated 3.6 years ago by
analeonpalacio
▴ 10 • written 15.8 years ago by
Tim Smith
★ 1.1k
0
votes
2
replies
958
views
problem using Alternative CDF environments, CdfEnvAffy
updated 15.8 years ago by
Martin Morgan
25k • written 15.8 years ago by
Vincent Davis
▴ 40
0
votes
1
reply
1.1k
views
Specifying a local CDF file for use with fitPLM or others
cdf
cdf
updated 15.8 years ago by
James W. MacDonald
68k • written 15.8 years ago by
Vincent Davis
▴ 40
0
votes
5
replies
1.8k
views
Imitating Affy's own steps
Microarray
Normalization
GO
Preprocessing
gcrma
Microarray
Normalization
GO
Preprocessing
updated 15.8 years ago by
James W. MacDonald
68k • written 15.8 years ago by
Timothy Wu
▴ 120
0
votes
0
replies
1.1k
views
stuck with affy/ limma
Clustering
genefilter
affy
limma
Clustering
genefilter
affy
limma
15.8 years ago
Maxim
▴ 170
0
votes
6
replies
1.6k
views
Error with read.maimages
limma
limma
updated 15.8 years ago by
Vincent J. Carey, Jr.
6.7k • written 15.8 years ago by
lapereir@uc.cl
▴ 30
0
votes
2
replies
1.0k
views
Embedding R output in Word
updated 15.8 years ago by
Sean Davis
21k • written 15.8 years ago by
Chintanu
▴ 310
0
votes
0
replies
1.2k
views
[MAANOVA] Contrasts for interaction levels - possible?
maanova
maanova
15.8 years ago
boczniak767
▴ 740
0
votes
0
replies
851
views
normalization
Kidney
Kidney
15.8 years ago
Yisong Zhen
▴ 200
0
votes
3
replies
1.5k
views
VSN: minimum number of controls?
Normalization
vsn
Normalization
vsn
updated 15.8 years ago by
Martin Morgan
25k • written 15.8 years ago by
Eric E. Snyder
▴ 20
0
votes
5
replies
1.7k
views
Biostrings C interface :: example not compiling
Biostrings
Biostrings
updated 15.8 years ago by
Charles Berry
▴ 290 • written 15.8 years ago by
Erik Wright
▴ 210
0
votes
0
replies
831
views
Using RMA normalization on 3 microarray replicates - valid?
Normalization
Normalization
15.8 years ago
James W. MacDonald
68k
46,732 results • Page
676 of 935
Recent ...
Replies
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
Awards
• All
Popular Question
to
shepherl
4.3k
Popular Question
to
ja569116
• 0
Popular Question
to
julia_mcdonough
• 0
Popular Question
to
Ahmed Salah
• 0
Popular Question
to
das.traveller
• 0
Locations
• All
United States,
7 minutes ago
United States,
40 minutes ago
Hungary,
49 minutes ago
Poland,
54 minutes ago
United States,
1 hour ago
Traffic: 1882 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