3
votes
4
replies
1.7k
views
Problem with scanBam
scanBam scanbamparam
updated 10.9 years ago by 25k • written 10.9 years ago by ▴ 150
0
votes
1
reply
1.7k
views
News: Course Announcement: Use R / Bioconductor for Sequence Analysis (Intermediate Course)
Course RNA-Seq Chip-seq Parallel News
10.9 years ago Martin Morgan 25k
4
votes
1
reply
3.3k
views
OFFICIAL_GENE_SYMBOL not an available idType in RDAVIDWebService
rdavidwebservice
updated 10.9 years ago by 68k • written 10.9 years ago by ▴ 30
0
votes
1
reply
1.3k
views
error with spliceR/cummberbund reading GTF file
software error
10.9 years ago knight2ni • 0
0
votes
3
replies
3.1k
views
Problem with reading raw Illumina Human HT-12 v4 data using beadarray
beadarray readIllumina
10.9 years ago jaro.slamecka ▴ 140
4
votes
4
replies
5.9k
views
Rsubread installation issues
rnaseq
10.9 years ago lshepard ▴ 40
2
votes
7
replies
3.5k
views
Removing samples from S4 object (in lumi)
lumi S4
10.9 years ago Chi Hong • 0
0
votes
11
replies
2.8k
views
FourCseq - error ountFragmentOverlaps()
fourcseq
10.9 years ago samuel collombet ▴ 140
1
vote
5
replies
2.0k
views
Understanding methyAnalysis Results
methyAnalysis methyanalysis methylation illuminahumanmethylation450k.db
updated 10.9 years ago by ▴ 80 • written 10.9 years ago by ▴ 370
0
votes
1
reply
2.1k
views
Adding Phenodata after processing in Lumi
PROcess lumi PROcess lumi
updated 10.9 years ago by • 0 • written 14.5 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Problem with gene annotation used in chimera package for fusion analysis
chimera package fusion genes annotation
10.9 years ago richa_r • 0
0
votes
10
replies
3.1k
views
Error when using readIDAT() from illuminaio
illuminaio idat
11.0 years ago • updated 10.9 years ago lacion • 0
4
votes
8
replies
4.8k
views
Visualising effects of observation/sample weights in differential expression analysis
limma voom sva edgeR
updated 10.9 years ago by ▴ 1000 • written 10.9 years ago by ▴ 20
1
vote
5
replies
2.5k
views
CRLMM on Illumina Human1Mv1_C chips
crlmm illumina beadarraysnp
updated 10.9 years ago by ▴ 1000 • written 10.9 years ago by ▴ 40
0
votes
1
reply
1.5k
views
reference manual "IlluminaHumanMethylation450kanno.ilmn12.hg19"
IlluminaHumanMethylation450kanno.ilmn12.hg19
10.9 years ago richa.gupta • 0
8
votes
4
replies
6.2k
views
limma - F-test for many condition
limma F-test
10.9 years ago samuel collombet ▴ 140
0
votes
11
replies
4.7k
views
Missing data after BiomaRt query
biomart bioconductor
updated 10.9 years ago by 16k • written 10.9 years ago by • 0
0
votes
2
replies
1.7k
views
DESEQ2 Gives Same Log2FC Across Multiple Sample Comparisons
deseq2
10.9 years ago gokhulkrishnakilaru • 0
0
votes
2
replies
2.4k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 10.9 years ago by ★ 1.6k • written 10.9 years ago by ▴ 100
0
votes
3
replies
3.3k
views
How to handle BSsmooth.tstat for single replicate samples? Error: need at least two non-NA values to interpolate
bsseq Bsmooth
updated 2.3 years ago by • 0 • written 10.9 years ago by • 0
0
votes
1
reply
2.1k
views
Job: Bioinformatics Post-Doc Positions
cancer BIOINFORMATICS genomics RNAseq miRseq Job
10.9 years ago aaron • 0
0
votes
0
replies
2.1k
views
Job: Services/Outreach orientend bioinformatics positions at EMBL - Heidelberg
EMBL services workflows training Job
10.9 years ago Wolfgang Huber ★ 13k
1
vote
2
replies
1.6k
views
problem of codelink
codelink
updated 10.9 years ago by ▴ 760 • written 10.9 years ago by ▴ 10
5
votes
6
replies
2.3k
views
Cannot find function treatDGE() in package edgeR?
edger installation
updated 10.9 years ago by 68k • written 10.9 years ago by • 0
1
vote
2
replies
2.5k
views
Deconvolution RNA-Seq data
rna-seq differential expression
updated 10.9 years ago by 68k • written 10.9 years ago by • 0
0
votes
1
reply
1.6k
views
riboSeqR: criteria used to determine reading frames
riboSeqR
updated 10.9 years ago by ▴ 180 • written 10.9 years ago by • 0
0
votes
1
reply
1.4k
views
riboSeqR: plotTranscript function not showing coverage
riboseqr
updated 10.9 years ago by ▴ 180 • written 10.9 years ago by • 0
2
votes
11
replies
20k
views
logfoldStandard Error and wald-statistics in DESeq2 results
deseq2 wald
updated 4.2 years ago by 43k • written 10.9 years ago by ▴ 20
2
votes
20
replies
6.5k
views
Important r packages not available for R version 3.1.1
exonmap exon array analysis bioconductor
10.9 years ago svlachavas ▴ 840
0
votes
3
replies
2.2k
views
problem with update limma - green channel missing
limma bioconductor read.maimages agilent 8x60K
10.9 years ago wd ▴ 30
5
votes
8
replies
2.6k
views
Missing mm10 in geneLenDataBase
geneLenDataBase mm10
updated 10.9 years ago by 16k • written 10.9 years ago by ▴ 40
0
votes
1
reply
1.5k
views
MAIT - suppress interactive mode
mait metabolomics
updated 10.9 years ago by ★ 8.2k • written 10.9 years ago by • 0
0
votes
5
replies
1.9k
views
Graphing coverage() results
ggbio genomicalignments bam
10.9 years ago gen ▴ 30
0
votes
5
replies
8.2k
views
Help required to install bioconductor in ubuntu
software error
updated 10.9 years ago by 16k • written 10.9 years ago by • 0
1
vote
4
replies
5.7k
views
problem with retrieving UniProt annotation data
uniprot.ws uniprot
updated 10.9 years ago by ★ 7.2k • written 10.9 years ago by ★ 4.1k
3
votes
12
replies
3.3k
views
performance issues when using readGAlignmentPairs with a ‘which’ argument
genomicalignments
11.0 years ago • updated 10.9 years ago Leonard Goldstein ▴ 90
3
votes
3
replies
5.2k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
11.0 years ago • updated 10.9 years ago samuel collombet ▴ 140
0
votes
4
replies
2.0k
views
[biomaRt] getBM: Error when obtaining mim_morbid_description
biomart getbm error
10.9 years ago Tibor Fulop • 0
10
votes
10
replies
8.6k
views
GLM Likelihood ratio test
rnaseq edgeR GLM
updated 10.9 years ago by 53k • written 10.9 years ago by • 0
4
votes
4
replies
2.7k
views
readVcfAsVRanges + FilterRules
variantannotation filterVcf readvcfasvranges filterRules
updated 10.9 years ago by 25k • written 10.9 years ago by ▴ 50
0
votes
3
replies
1.4k
views
Problem with mcols in GenomicFeatures
genomicfeatures
10.9 years ago Jake ▴ 90
0
votes
7
replies
4.6k
views
Error in loading R package topgo
topgo
updated 10.9 years ago by 25k • written 10.9 years ago by • 0
2
votes
2
replies
1.8k
views
Target version of R for Bioconductor 3.1?
new version
10.9 years ago David Eby ▴ 30
0
votes
1
reply
1.8k
views
meta-analysis of RNA-seq data
deseq2 rna-seq
10.9 years ago anpham ▴ 70
3
votes
4
replies
1.9k
views
DESeq2 detects DE when expression is 0 under both contrast levels
deseq2 rnaseq r
updated 10.9 years ago by 43k • written 10.9 years ago by • 0
1
vote
2
replies
2.9k
views
Supervised clustering by sample
hclust heatmap
10.9 years ago rmgreer • 0
0
votes
2
replies
2.6k
views
How to specifiy colors for polygon links when using circos function of OmicCircos package
graph omiccircos
updated 10.9 years ago by ▴ 50 • written 10.9 years ago by • 0
0
votes
3
replies
991
views
limma common reference
limma
updated 10.9 years ago by 68k • written 10.9 years ago by • 0
2
votes
10
replies
3.5k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
11.0 years ago • updated 10.9 years ago n.kreim ▴ 20
4
votes
6
replies
3.2k
views
How to mport publically available RMA processed dataset (on ArrayExpress) into Limma?
limma microarray
updated 10.9 years ago by ★ 29k • written 10.9 years ago by ▴ 10
46,738 results • Page 468 of 935
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Replies
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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