3
votes
4
replies
4.2k
views
Can't make working link in roxygen2
roxygen2
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ▴ 370
8
votes
4
replies
7.6k
views
Can't upgrade to Bioconductor 3.3?
bioconductor biocupgrade upgrade update bioclite
9.7 years ago enricoferrero ▴ 680
0
votes
0
replies
1.0k
views
Analysis of Various chemical compounds on Cytotoxity Cell lines
clustering normalization
9.7 years ago ramars • 0
1
vote
3
replies
2.5k
views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
9.7 years ago Hugo Varet ▴ 80
0
votes
2
replies
1.6k
views
Error in processAmplicons "hairpin sequence length not with specified length"
processamplicons
updated 9.7 years ago by ▴ 1000 • written 9.7 years ago by • 0
1
vote
6
replies
3.2k
views
different results between Rsamtools::pileup and samtools depth
rsamtools pileup
9.7 years ago TimothéeFlutre ▴ 80
0
votes
5
replies
878
views
multifactor edgeR logFC
edger
9.7 years ago tminning • 0
0
votes
1
reply
1.4k
views
flowCore: specify polygon coordinates
polygon gate flowcore flowviz
updated 9.7 years ago by 4.3k • written 9.7 years ago by • 0
1
vote
2
replies
1.6k
views
DEXSeq. Error: could not find function "DEXSeqDataSetFromHTSeq"
dexseq
9.7 years ago peter.thorpe • 0
2
votes
3
replies
1.8k
views
Can we use Entrez IDs for GOSeq?
goseq entrez gene identifiers
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
0
votes
1
reply
1.4k
views
rsbml: can not link to SUNDIALS
rsbml
9.7 years ago ivo • 0
1
vote
1
reply
2.4k
views
CellMix compare results to CellCODE
cellmix cellcode
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ▴ 20
6
votes
10
replies
3.4k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 21 months ago by • 0 • written 9.7 years ago by ▴ 180
1
vote
1
reply
1.4k
views
DESeqDataSet creation error
deseq2
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 70
1
vote
2
replies
1.8k
views
Workflows in BioC 3.3
workflows workflowinstall 3.3
9.7 years ago Axel Klenk ★ 1.1k
1
vote
3
replies
3.3k
views
DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
deseq2 rnaseq rna-seq normalization cpm
updated 9.7 years ago by ★ 13k • written 9.7 years ago by • 0
1
vote
8
replies
2.5k
views
Understanding the design matrix
deseq2 design and contrast matrix
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 30
2
votes
4
replies
2.6k
views
Getting gene ID's from camera results
limma camera
updated 9.7 years ago by ▴ 150 • written 9.7 years ago by ▴ 110
3
votes
14
replies
5.1k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina
updated 9.7 years ago by ▴ 890 • written 9.7 years ago by • 0
1
vote
5
replies
16k
views
Limma LogFC hand calculation
limma logfc
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
2
votes
8
replies
2.4k
views
Regarding Somatic Mutation Signature
somaticsignatures
updated 9.7 years ago by ★ 1.3k • written 9.8 years ago by ▴ 10
4
votes
7
replies
2.8k
views
Understanding the output of the exprs() function
affymetrix microarrays
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
2
votes
2
replies
3.1k
views
Error during installation of ChemmineOB R package
Chemmine Ubuntu OpenBabel
updated 9.7 years ago by ★ 1.7k • written 9.7 years ago by ▴ 10
1
vote
4
replies
1.6k
views
rtrackylayer import bedpe error
rtracklayer
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 200
2
votes
1
reply
1.4k
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 40
1
vote
2
replies
2.2k
views
how to convert emsembl identiers with ENTERz ID in a logfoldchange files generated by DESeq2 to be used for SPIA
runspia deseq2 ENTerz
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
4
votes
9
replies
3.3k
views
LIMMA gives different logFC
limma LogFC
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
0
votes
5
replies
2.4k
views
Install SomaticSignatures (ERROR: compilation failed for package 'RBGL')
somaticsignatures RGBL
9.7 years ago user31888 ▴ 30
1
vote
4
replies
1.8k
views
Error with wavClusteR annotateClusters function
wavcluster
updated 9.7 years ago by ▴ 100 • written 9.7 years ago by ▴ 10
0
votes
1
reply
1.9k
views
DEXSeq and shrinkage diagnostic : Comparison between results in plotDispEsts( dxd )
dexseq estimatedispersions
updated 9.7 years ago by ★ 13k • written 9.8 years ago by • 0
0
votes
1
reply
1.6k
views
interpreting dispersion estimation in dexseq
deseq2 dexseq estimatedispersions
updated 9.7 years ago by ★ 13k • written 9.8 years ago by ★ 1.5k
2
votes
4
replies
2.3k
views
supportedUCSCtables(genome="hg38"): Is ensGene track really available?
genomicfeatures
updated 9.7 years ago by 16k • written 9.8 years ago by ▴ 40
4
votes
10
replies
1.8k
views
Extremely Big Number of Differences from Multi-level Design in RNA-seq Analysis by both Limma and DESeq2 - Something wrong with the design?
limma deseq2
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 10
1
vote
7
replies
27k
views
getting error with DEseq2
deseq2
9.7 years ago Nemo ▴ 80
0
votes
1
reply
1.0k
views
genome searching with Biostrings and the BSgenome data packages
biostrings
updated 9.7 years ago by 25k • written 9.8 years ago by • 0
0
votes
2
replies
2.8k
views
Advice on normalization with metagenomics data
metagenome normalization metagenomics
9.7 years ago David ▴ 860
2
votes
30
replies
5.8k
views
create design matrix when 2 groups of gene-expression data
limma
10.1 years ago • updated 9.7 years ago mheydarpour ▴ 10
0
votes
1
reply
2.0k
views
How to identify the microarray annotation library automatically from GEO study ID?
limma microarray annotation bioconductor annotate
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
0
votes
1
reply
1.9k
views
Problem loading minfi on macOS
minfi minfidata rgl. mac os x el capitan
updated 9.7 years ago by ★ 6.5k • written 9.7 years ago by • 0
6
votes
6
replies
2.5k
views
genefilter filtered out 60% of the original genes?
genefilter edgeR
updated 9.7 years ago by ▴ 180 • written 9.8 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Possible bug in ConsensusSequence
DECIPHER
updated 9.7 years ago by ▴ 10 • written 9.7 years ago by • 0
0
votes
3
replies
2.1k
views
GSVA (1.18.0) segfaulting on small dataset
gsva segfault
updated 9.7 years ago by ★ 3.4k • written 9.7 years ago by ▴ 120
1
vote
3
replies
1.6k
views
DESeq2 robust fpkm error with tximport
DESeq2
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
0
votes
0
replies
1.0k
views
normalizing gene expression data with TCGAbiolinks
microarray tcgabiolinks rnaseq
9.7 years ago Fernando • 0
1
vote
1
reply
1.8k
views
Error using nsFilter() Error in (function (classes, fdef, mtable) unable to find an inherited method for function columns for signature function
genefilter
9.7 years ago Lucy • 0
1
vote
2
replies
1.8k
views
mRNA start used instead of gene start in makeTxDbFromGFF
maketxdbfromgff genomicfeatures
updated 9.7 years ago by 16k • written 9.8 years ago by ▴ 80
2
votes
1
reply
1.4k
views
Error in score() function on pairwiseAlignment()
biostrings pairwisealignment
updated 9.7 years ago by 4.3k • written 9.8 years ago by • 0
3
votes
5
replies
9.4k
views
Wgcna with missing values - error with calculation of bicor correlations in pickSoftThreshold and blockwiseModules
software error rnaseq wgcna missing data
10.1 years ago • updated 9.7 years ago dvillarlozano ▴ 10
0
votes
5
replies
2.7k
views
arrayExpress: problem running code from the vignette
arrayexpress
9.8 years ago kevin.rue ▴ 350
1
vote
5
replies
2.4k
views
openCyto - flowclust.2d throws errors
opencyto flow cytometry
updated 9.8 years ago by • 0 • written 9.8 years ago by ▴ 30
46,738 results • Page 397 of 935
Recent ...
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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