0
votes
1
reply
1.8k
views
Calculation of $stdev.unscaled and $sigma values by lmfit() in Limma package
updated 15.8 years ago by ★ 7.4k • written 15.8 years ago by ▴ 10
1
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3
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1.2k
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Get gene structure information: use biomaRt or other annotation packages?
Annotation biomaRt Annotation biomaRt
updated 15.8 years ago by ★ 3.4k • written 15.8 years ago by ★ 4.3k
0
votes
0
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1.1k
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MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
15.8 years ago Gordon Smyth 53k
0
votes
2
replies
925
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GO.db and org.XX.eg.db: update frequency?
Annotation GO Annotation GO
updated 15.8 years ago by 25k • written 15.8 years ago by ★ 4.3k
0
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2
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1.1k
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xps: returns only 21 records
Preprocessing Preprocessing
updated 15.8 years ago by ★ 3.9k • written 15.8 years ago by ▴ 330
0
votes
1
reply
1.6k
views
GEOquery problem
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 50
0
votes
0
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1.1k
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request: calculate coverage with weight on RangedData object
Coverage Cancer IRanges Coverage Cancer IRanges
15.8 years ago Janet Young ▴ 740
0
votes
1
reply
1.5k
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SPIA package
graph SPIA graph SPIA
updated 15.8 years ago by ★ 7.4k • written 15.8 years ago by ▴ 200
0
votes
1
reply
1.0k
views
MArray into data.frame for SPIA package
limma limma
updated 15.8 years ago by ★ 7.4k • written 15.8 years ago by ▴ 200
0
votes
0
replies
2.1k
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Job: Bioinformatics Data Analyst in Vienna, Austria
15.8 years ago Ido M. Tamir ▴ 320
0
votes
2
replies
907
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Tools for comparing microarray data on a snp level
SNP cdf SNP cdf
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 40
0
votes
0
replies
1.0k
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A statistical analyst or a post-doctoral position available immediately at Northwestern University
15.8 years ago Pan Du ★ 1.2k
0
votes
10
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2.7k
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microRNA: which genes code for a specific mirna?
miRNA GO microRNA miRNA GO microRNA
updated 15.8 years ago by ▴ 830 • written 15.8 years ago by ★ 1.1k
0
votes
8
replies
2.0k
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IRanges: cbind not well defined for RangedData?
updated 15.8 years ago by ★ 11k • written 15.8 years ago by ▴ 550
0
votes
2
replies
1.2k
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IRanges: setting score() on RangedData drops rownames
updated 15.8 years ago by ★ 1.6k • written 15.8 years ago by ▴ 550
0
votes
0
replies
891
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Favor: ChIPpeakAnno
PROcess PROcess
15.8 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
871
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CN analysis on a small Affymetrix GWS6 data set (Was: Re: QC Affy 6.0 SNP arrays with crlmm or Oligo?)
Preprocessing Preprocessing
15.8 years ago Henrik Bengtsson ★ 2.4k
0
votes
1
reply
1.1k
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limma lmFit error: Coefficients not estimable
limma limma
15.8 years ago Freydin, Maxim ▴ 30
0
votes
6
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2.0k
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QC Affy 6.0 SNP arrays with crlmm or Oligo?
Normalization oligo crlmm Normalization oligo crlmm
updated 15.8 years ago by ★ 4.3k • written 15.8 years ago by ▴ 150
0
votes
8
replies
2.7k
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hclust for 13000 genes
updated 15.8 years ago by ★ 13k • written 15.8 years ago by ▴ 240
0
votes
12
replies
4.2k
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problems when trying to use biomaRt
GUI biomaRt GUI biomaRt
updated 15.8 years ago by ★ 2.0k • written 15.8 years ago by ▴ 50
0
votes
5
replies
1.5k
views
package or code to quantify the significance of the venn overlap between 2 or 3 lists of genes
updated 15.8 years ago by ★ 13k • written 15.8 years ago by ▴ 420
0
votes
1
reply
738
views
Package for Agilent microdata
updated 15.8 years ago by ★ 13k • written 15.8 years ago by ▴ 10
0
votes
3
replies
2.5k
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getGEO - getting the .CEL files from GEO
Microarray Microarray
updated 15.8 years ago by 6.7k • written 15.8 years ago by ▴ 10
0
votes
2
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1.7k
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AgiMicroRna package is not available at bioconductor or not in active form???
Microarray Network microRNA AgiMicroRna Microarray Network microRNA AgiMicroRna
updated 15.8 years ago by ▴ 60 • written 15.8 years ago by 21k
0
votes
0
replies
1.4k
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SNP plotter package
SNP SNP
15.8 years ago Kay Jaja ▴ 90
0
votes
0
replies
918
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FW: Bioconductor
affy oligo affy oligo
15.8 years ago Dana.Stanley@csiro.au ▴ 110
0
votes
1
reply
1.2k
views
AffyPLM's MAplot and cex
updated 15.8 years ago by ★ 1.2k • written 15.8 years ago by ▴ 120
0
votes
0
replies
932
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Fwd: problems when trying to use biomaRt
GUI biomaRt GUI biomaRt
15.8 years ago Sean Davis 21k
0
votes
1
reply
1.1k
views
multicore package and AnnotationDbi
GO rat2302 AnnotationDbi GO rat2302 AnnotationDbi
updated 15.8 years ago by 6.7k • written 15.8 years ago by ▴ 10
0
votes
1
reply
1.6k
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log Fold Change
limma limma
updated 15.8 years ago by ★ 3.4k • written 15.8 years ago by ▴ 10
0
votes
4
replies
1.9k
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Reg: T-statistic using limma
PROcess PROcess
15.8 years ago Rohit Farmer ▴ 170
0
votes
8
replies
2.3k
views
(no subject)
limma limma
updated 15.8 years ago by ▴ 240 • written 15.8 years ago by ▴ 40
0
votes
0
replies
876
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affymetrix gene level arrays - cdf issue
cdf xps cdf xps
15.8 years ago Stefanie Tauber ▴ 40
0
votes
6
replies
1.7k
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farms package fails on estrogen data
Preprocessing Preprocessing
updated 15.8 years ago by 25k • written 15.8 years ago by ▴ 840
0
votes
0
replies
929
views
rawQ Affymetrix
15.8 years ago Dr Gyorffy Balazs ▴ 320
0
votes
4
replies
3.7k
views
Problems with Downloading packages
updated 15.8 years ago by 25k • written 15.8 years ago by ▴ 70
0
votes
0
replies
1.2k
views
LIMMA Array Weight analysis
Microarray Normalization limma Microarray Normalization limma
15.8 years ago GAO Yu ▴ 10
0
votes
1
reply
1.2k
views
AgiMicroRna package is not available at bioconductor or not in active form???
Microarray microRNA Microarray microRNA
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 100
0
votes
7
replies
2.2k
views
about formula in ancova
15.8 years ago De-Jian ZHAO ▴ 240
0
votes
1
reply
782
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Problems installing Bioconductor Affy on Windows 7
affy limma affy limma
updated 15.8 years ago by 25k • written 15.8 years ago by ▴ 10
0
votes
1
reply
1.6k
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extract intensity values from .cel using Affy probe ids
Normalization probe Normalization probe
updated 15.8 years ago by ★ 2.4k • written 15.8 years ago by ▴ 30
0
votes
0
replies
836
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a new bridge between bioperl and bioconductor
15.8 years ago Zheng, Xin NIH [C] ▴ 30
0
votes
5
replies
2.5k
views
snapCGH, runBioHMM, Error: segfault from C stack overflow
snapCGH snapCGH
updated 15.8 years ago by ▴ 150 • written 15.8 years ago by ▴ 100
0
votes
4
replies
1.6k
views
Limma-Contrasts-Question
limma limma
updated 15.8 years ago by ▴ 30 • written 15.8 years ago by 53k
0
votes
0
replies
956
views
silent data corruption in flowFlowJo, and fix
flowFlowJo flowFlowJo
15.8 years ago Hin-Tak Leung ▴ 30
0
votes
11
replies
2.7k
views
Issue with limma and normalization of Agilent data generated with a 20-bit scan
Normalization limma marray Normalization limma marray
updated 15.8 years ago by 53k • written 15.8 years ago by ▴ 130
0
votes
3
replies
2.0k
views
[MAANOVA] Warnings in fitmaanova & information request
maanova oligo maanova oligo
15.8 years ago boczniak767 ▴ 740
0
votes
0
replies
891
views
limma: duplicate spots, technical replicates and biological replicates
limma limma
15.8 years ago Ana Staninska ▴ 40
0
votes
1
reply
3.6k
views
color key - heatmap.2
Coverage Coverage
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 10
46,695 results • Page 678 of 934
Recent ...
Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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