0
votes
2
replies
4.0k
views
using Blat in R
Alignment PROcess Alignment PROcess
updated 15.8 years ago by ★ 1.9k • written 15.8 years ago by ▴ 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 ★ 11k • written 15.8 years ago by ★ 3.4k
0
votes
1
reply
1.0k
views
normalization between different microarray
updated 15.8 years ago by ▴ 970 • written 15.8 years ago by ▴ 50
0
votes
3
replies
2.4k
views
Help please: FCS binary to ascii text using bioconductor
updated 15.8 years ago by ▴ 140 • written 15.8 years ago by ▴ 340
0
votes
2
replies
984
views
Recycling vars with IRanges::reflect
Cancer IRanges Cancer IRanges
updated 15.8 years ago by ★ 1.6k • written 15.8 years ago by ★ 13k
0
votes
4
replies
1.4k
views
RNA degradation plot
graph graph
updated 15.8 years ago by ★ 4.3k • written 15.8 years ago by ★ 1.5k
0
votes
4
replies
2.9k
views
snow library, question on clusterExport
updated 15.8 years ago by ▴ 70 • written 15.8 years ago by ▴ 200
0
votes
11
replies
2.3k
views
Problems in MAplot for affybatch objects
updated 15.8 years ago by ★ 1.2k • written 15.8 years ago by ▴ 840
0
votes
8
replies
3.0k
views
'SRAdb useful for visualizing BAM files'
SRAdb SRAdb
updated 15.8 years ago by ▴ 170 • written 15.8 years ago by ★ 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 ★ 1.1k • written 15.8 years ago by ▴ 340
0
votes
1
reply
1.0k
views
installation of Rgraphviz
Rgraphviz Rgraphviz
updated 15.8 years ago by ★ 6.5k • written 15.8 years ago by ▴ 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 ★ 4.3k • written 15.8 years ago by ▴ 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 ★ 7.2k • written 15.8 years ago by ▴ 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 21k • written 15.8 years ago by ▴ 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 ★ 11k • written 15.8 years ago by ★ 1.1k
0
votes
2
replies
1.2k
views
error in import.exon.scheme, XPS package
xps xps
updated 15.8 years ago by ★ 3.9k • written 15.8 years ago by ▴ 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 68k • written 15.8 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Query regarding GEO Database
ArrayExpress ArrayExpress
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 120
0
votes
6
replies
2.0k
views
load failed for 'Rlibstree'
hgu133plus2 rtracklayer hgu133plus2 rtracklayer
updated 15.8 years ago by ★ 7.4k • written 15.8 years ago by ★ 1.1k
0
votes
1
reply
4.7k
views
Mapping onto KO numbers (KEGG Orthology)
updated 15.8 years ago by 68k • written 15.8 years ago by ▴ 60
0
votes
2
replies
1.7k
views
memory allocation problem not solved
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 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 6.7k • written 15.8 years ago by ★ 4.1k
0
votes
2
replies
1.1k
views
BioC packages for Human Gene 1.0 ST arrays
updated 15.8 years ago by ▴ 630 • written 15.8 years ago by ▴ 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 ▴ 630 • written 15.8 years ago by ▴ 820
0
votes
6
replies
3.4k
views
Error in GO.db
GO GO
updated 15.8 years ago by 6.7k • written 15.8 years ago by ▴ 510
0
votes
6
replies
3.1k
views
consensusString Function
updated 15.8 years ago by ★ 1.6k • written 15.8 years ago by ▴ 210
0
votes
1
reply
1.1k
views
Query regarding memory allocation
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 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 21k • written 15.8 years ago by ▴ 70
0
votes
1
reply
834
views
Query
cdf probe cdf probe
updated 15.8 years ago by 68k • written 15.8 years ago by ▴ 220
0
votes
2
replies
1.0k
views
Query regarding Bioconductor package
Microarray Microarray
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 120
0
votes
2
replies
1.4k
views
Methylation data
updated 15.8 years ago by ▴ 260 • written 15.8 years ago by ▴ 250
0
votes
9
replies
2.5k
views
Error with unique
Biostrings Biostrings
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 210
0
votes
6
replies
3.6k
views
converting position from '-' strand to '+' strand
convert convert
updated 3.6 years ago by ▴ 10 • written 15.8 years ago by ★ 1.1k
0
votes
2
replies
958
views
problem using Alternative CDF environments, CdfEnvAffy
updated 15.8 years ago by 25k • written 15.8 years ago by ▴ 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 68k • written 15.8 years ago by ▴ 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 68k • written 15.8 years ago by ▴ 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 6.7k • written 15.8 years ago by ▴ 30
0
votes
2
replies
1.0k
views
Embedding R output in Word
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 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 25k • written 15.8 years ago by ▴ 20
0
votes
5
replies
1.7k
views
Biostrings C interface :: example not compiling
Biostrings Biostrings
updated 15.8 years ago by ▴ 290 • written 15.8 years ago by ▴ 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