0
votes
2
replies
1.2k
views
Anyone thinking of expanding rsbml capability of reading SBML versions?
updated 15.2 years ago by ★ 11k • written 15.2 years ago by ▴ 60
0
votes
0
replies
1.2k
views
Questions about model matrix, logFC and adjusted P.value of t-test
15.2 years ago Mingkwan Nipitwattanaphon ▴ 30
0
votes
1
reply
1.1k
views
the issue with analysis of multi-channel screen
updated 15.2 years ago by ★ 13k • written 15.2 years ago by ▴ 80
0
votes
2
replies
1.6k
views
Problem importing ArrayExpress data for custom array into BioConductor
Microarray cdf ArrayExpress Microarray cdf ArrayExpress
updated 15.2 years ago by ★ 13k • written 15.2 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Using rtracklayer for ranges of Genomic DNA
rtracklayer rtracklayer
updated 15.2 years ago by ★ 11k • written 15.2 years ago by ▴ 30
0
votes
2
replies
1.9k
views
HTqPCR : readCtData problem?
miRNA qPCR HTqPCR miRNA qPCR HTqPCR
15.2 years ago Heidi Dvinge ★ 2.0k
0
votes
1
reply
1.2k
views
Package xps: problem with RMA normalization for Human Gene ST 1.0
Annotation Normalization xps Annotation Normalization xps
updated 15.2 years ago by ▴ 80 • written 15.2 years ago by ★ 3.9k
0
votes
2
replies
1.5k
views
need help on
limma limma
updated 15.2 years ago by ▴ 340 • written 15.2 years ago by ▴ 890
0
votes
0
replies
604
views
Package gpls_1.22.0.tar.gz has been built for Windows
15.2 years ago Uwe.Ligges@r-project.org ▴ 120
0
votes
0
replies
606
views
Package Icens_1.22.0.tar.gz has been built for Windows
15.2 years ago Uwe.Ligges@r-project.org ▴ 120
0
votes
0
replies
1.1k
views
Package xps: problem with RMA normalization for Human Gene ST 1.0
Normalization xps Normalization xps
15.2 years ago Naïma Oumouhou ▴ 80
0
votes
0
replies
1.4k
views
HTqPCR problem
qPCR GO HTqPCR qPCR GO HTqPCR
15.2 years ago Heidi Dvinge ★ 2.0k
0
votes
0
replies
1.1k
views
Human Affymetrix Exon microarrays
exonmap exonmap
15.2 years ago Ernest Turro ▴ 30
0
votes
0
replies
974
views
ChIPpeakAnno
ChIPpeakAnno ChIPpeakAnno
15.2 years ago Julie Zhu ★ 4.3k
0
votes
7
replies
1.6k
views
Rsamtools from biocLite using R-devel
Rsamtools Rsamtools
updated 15.2 years ago by 25k • written 15.2 years ago by ★ 6.5k
0
votes
4
replies
1.6k
views
Cyclic Loess
Microarray Microarray
15.2 years ago viritha kaza ▴ 580
0
votes
3
replies
1.3k
views
gene-locations
cdf cdf
updated 15.2 years ago by 68k • written 15.2 years ago by ▴ 100
0
votes
1
reply
1.3k
views
GEOquery: Best way to get a phenodata table from GSE
Cancer Cancer
updated 15.2 years ago by 21k • written 15.2 years ago by ★ 1.9k
0
votes
1
reply
1.0k
views
duplicated on IRanges object
IRanges IRanges
updated 15.2 years ago by 16k • written 15.2 years ago by ▴ 10
0
votes
2
replies
1.5k
views
method and package for imputing spectral counts from masspectrometry
updated 15.2 years ago by ▴ 120 • written 15.2 years ago by ▴ 120
0
votes
5
replies
1.7k
views
intermittent oddity in rtracklayer track names
trigger trigger
updated 15.2 years ago by ★ 11k • written 15.2 years ago by ★ 1.1k
0
votes
0
replies
1.0k
views
Course: Introduction to R / Bioconductor, Seattle Dec 9 / 10
Cancer Cancer
15.2 years ago Martin Morgan 25k
0
votes
1
reply
799
views
Affy/annaffy question
updated 15.2 years ago by 68k • written 15.2 years ago by ▴ 170
0
votes
3
replies
1.3k
views
rtracklayer -- how to hide some default tracks? fine-grained control of track view mode (pack, full, dense, squish...)
BSgenome BSgenome BSgenome BSgenome
updated 15.2 years ago by ★ 11k • written 15.2 years ago by ★ 1.1k
0
votes
3
replies
935
views
A story about IRanges::GappedRanges ... how does it end?
Cancer IRanges Cancer IRanges
updated 15.2 years ago by ★ 11k • written 15.2 years ago by ★ 13k
0
votes
3
replies
1.1k
views
Combining two CompressedNormalIRangesList objects doesn't work
Cancer IRanges Cancer IRanges
15.2 years ago Steve Lianoglou ★ 13k
0
votes
0
replies
1.5k
views
Normalization using dCHIP
15.2 years ago Lakshmi Kastury ▴ 40
0
votes
5
replies
2.6k
views
Package plgem for analysis of spectral counts, was 'limma for spectral counts'
Microarray Proteomics limma plgem Microarray Proteomics limma plgem
updated 15.2 years ago by ▴ 120 • written 15.2 years ago by ▴ 70
4
votes
4
replies
2.7k
views
limma for spectral counts
limma limma
updated 15.2 years ago by ▴ 70 • written 15.2 years ago by ▴ 120
0
votes
2
replies
1.5k
views
EdgeR - problems running estimateCRDisp
RNASeq edgeR RNASeq edgeR
updated 15.2 years ago by 53k • written 15.2 years ago by ▴ 60
0
votes
4
replies
1.4k
views
GRangesForUCSCGenome seems to be missing in rtracklayer 1.10, GenomicRanges 1.2
BSgenome BSgenome rtracklayer BSgenome BSgenome rtracklayer
updated 15.2 years ago by 6.7k • written 15.2 years ago by ★ 1.1k
0
votes
2
replies
1.4k
views
Loading Niblegen Files to Oligo
oligo oligo
updated 15.2 years ago by ★ 4.3k • written 15.2 years ago by ▴ 10
0
votes
0
replies
525
views
Biobase in R 2.12 referencing libR.dylib from R 2.11, bug?
15.2 years ago John Brehm ▴ 10
0
votes
1
reply
1.4k
views
how to map affy SNP ID to pubmed ID
SNP Annotation affy SNP Annotation affy
updated 15.2 years ago by ★ 7.2k • written 15.2 years ago by ▴ 110
0
votes
3
replies
1.5k
views
strange ChIPpeakAnno and rtracklayer interaction.
GO annotate rtracklayer ChIPpeakAnno GO annotate rtracklayer ChIPpeakAnno
updated 15.2 years ago by ★ 11k • written 15.2 years ago by ▴ 20
0
votes
3
replies
1.6k
views
getNetAffx function when using oligo package
Annotation Annotation
updated 15.2 years ago by 68k • written 15.2 years ago by ▴ 20
0
votes
0
replies
1.1k
views
grid.chromosome in quantsmooth, without cytobands?
idiogram idiogram
15.2 years ago Paul Shannon ★ 1.1k
0
votes
0
replies
1.1k
views
error with MEDIPS.CpGenrich -> resize + segfault in MEDIPS.plotCalibrationPlot
BSgenome BSgenome MEDIPS BSgenome BSgenome MEDIPS
15.2 years ago Nora ▴ 20
0
votes
0
replies
997
views
Annotation package for affy SNP6.0
SNP probe affy SNP probe affy
15.2 years ago Qian Liu ▴ 110
0
votes
1
reply
1.1k
views
Question about subtracks shown using ‘rtracklayer’ package
updated 15.2 years ago by ★ 11k • written 15.2 years ago by ▴ 450
0
votes
1
reply
1.5k
views
biomaRt query : inconsistent results for different Attribute set
Annotation Annotation
updated 15.2 years ago by ▴ 500 • written 15.2 years ago by ▴ 260
0
votes
0
replies
1.4k
views
Downloading metabolic pathway data from KEGG
Network graph Network graph
15.2 years ago Tim Clough ▴ 10
0
votes
1
reply
1.6k
views
error in library(affy)
updated 15.2 years ago by 25k • written 15.2 years ago by ▴ 510
0
votes
2
replies
1.0k
views
AnnotatedDataFrame and cbind
Biobase Biobase
updated 15.2 years ago by 6.7k • written 15.2 years ago by ★ 3.8k
0
votes
2
replies
1.1k
views
arrayQualityMetrics 3.2.0 in Bioc release 2.7 is broken
updated 15.2 years ago by ▴ 230 • written 15.2 years ago by ★ 13k
0
votes
0
replies
1.5k
views
Bioconductor
cdf affy affyPara cdf affy affyPara
15.2 years ago Valerie Obenchain ★ 6.8k
0
votes
0
replies
1.3k
views
ChIPpeakAnno bug?
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
15.2 years ago Julie Zhu ★ 4.3k
0
votes
4
replies
4.9k
views
*** caught segfault *** ....cause 'invalid permissions' with PUMA pachage
puma puma
15.2 years ago Alberto Goldoni ▴ 420
0
votes
1
reply
994
views
(no subject)
exonmap xmapcore exonmap xmapcore
updated 15.2 years ago by ★ 7.2k • written 15.2 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Error while ChIPpeakAnno installation
limma biomaRt IRanges ChIPpeakAnno limma biomaRt IRanges ChIPpeakAnno
updated 15.2 years ago by ★ 4.3k • written 15.2 years ago by ▴ 260
46,717 results • Page 653 of 935
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Replies
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…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 20
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
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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Commentator to James W. MacDonald 68k
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