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Unable to find an inherited method for function 'results' for signature '"DESeqDataSet"'
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
1
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sva correction for MEDIPS
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updated 7.0 years ago by ▴ 570 • written 7.0 years ago by • 0
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Setting gene expression thresholds for trajectory analysis using Monocle
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7.0 years ago S.Webb6 ▴ 40
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How to retreive topGO significant IDs of genes after enrichment test ?
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7.0 years ago David ROUX ▴ 20
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Limma import array layout GenePix files
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updated 7.0 years ago by 53k • written 7.0 years ago by • 0
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referencePrepare function in IntEREst package
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7.0 years ago eva.pinatel ▴ 10
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Error in Champ for Bioconductor performing GSEA analysis on Methlayion array data
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updated 7.0 years ago by • 0 • written 7.0 years ago by • 0
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justRMA and wrong customCDFs causing segfault
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updated 7.0 years ago by ▴ 10 • written 10.2 years ago by • 0
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Error in Champ for Bioconductor and ChAMP.Block() analysis 450K methylation data
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Retrieve canonical transcript for each gene via ensembldb R package
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updated 3.5 years ago by ▴ 40 • written 7.0 years ago by • 0
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Taking into account strong batch effect in microarray differential expression analysis with limma
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How to change stringtie gene_id names with ref_gene_id when performing featureCount
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updated 7.0 years ago by ★ 3.6k • written 7.0 years ago by • 0
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7.0 years ago bioinfo • 0
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Matching GenBank Accession Number with corresponding Biomart results
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updated 7.0 years ago by 68k • written 7.0 years ago by • 0
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vennDiagram in Limma package
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updated 7.0 years ago by 68k • written 7.0 years ago by • 0
2
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How to calculate overlap between transposable elements differentially expressed in one experiment, with those expressed in another set of samples?
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updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 40
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updated 7.0 years ago by 43k • written 7.0 years ago by • 0
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DESeq2: Including known contaminant in the design model does not change PCA plot
deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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DESeq2 for analyzing differential expression based on dispersion across samples within groups, instead of based on expression means.
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updated 7.0 years ago by 43k • written 7.0 years ago by • 0
5
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10
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what should I do with many zero counts from Salmon quantification
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updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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how to handle missing data for SampleTable in DESeq2
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updated 7.0 years ago by • 0 • written 10.8 years ago by ▴ 70
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updated 7.0 years ago by 68k • written 7.0 years ago by • 0
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Dealing with HSP in blast output with GRanges
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updated 7.0 years ago by 25k • written 7.0 years ago by • 0
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RefGate populations switched in OpenCyto 1.20
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updated 7.0 years ago by ★ 1.3k • written 7.1 years ago by • 0
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Identify Core packages
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7.0 years ago cszamudio • 0
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updated 7.0 years ago by 68k • written 7.0 years ago by • 0
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Overall genes number in the TissueEnrich package output
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updated 7.0 years ago by ▴ 10 • written 7.0 years ago by • 0
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Limma filtering low expressed probes
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updated 7.0 years ago by 53k • written 7.0 years ago by • 0
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newSCESet(countData=all.counts) function not working
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Different results with DESeq2 and EdgeR
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7.0 years ago AZ ▴ 20
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Is it allowed to fit two models to make between and within subjects comparisons separately?
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7.0 years ago tcalvo ▴ 100
0
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package for mismatch distribution?
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Different DEG results using Ballgown and edgeR
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updated 7.0 years ago by 53k • written 7.0 years ago by • 0
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Results table completely wrong for specified contrast of
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updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 60
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GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
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updated 7.0 years ago by 21k • written 7.0 years ago by ▴ 20
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Deseq2: How to compine reseult of different pairwise comparisons
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updated 7.0 years ago by 43k • written 7.0 years ago by • 0
1
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different observation of DEG for same group
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updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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DESeq2 LRT test behaving strangely?
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7.0 years ago casikecola • 0
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biomaRt bug report
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updated 7.0 years ago by ★ 6.6k • written 7.0 years ago by • 0
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Rsubread- feature counts
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updated 7.0 years ago by 53k • written 7.0 years ago by • 0
2
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edgeR DEG how many treatments should be fitted to GLM
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updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 10
0
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772
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regioneR ignore the strand information when using the extendRegions() function
regionR extendRegions
updated 7.0 years ago by ▴ 150 • written 7.1 years ago by • 0
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Pre-processing RNA-seq data (normalization and transformation) for GSVA
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7.8 years ago • updated 7.0 years ago rached ▴ 60
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MSnbase package, Error in downloading data file "PXD000001" from PRIDE Repository by pxget function
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updated 3.7 years ago by 1.6k • written 7.0 years ago by ▴ 10
0
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0
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unwanted linebreaks using write.table with a dataframe created via the myvariant.info r package
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updated 7.0 years ago by 4.3k • written 7.0 years ago by • 0
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Need expert suggestion about Bioconductor package for microarray data anlaysis
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edgeR DEG sample size
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updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 10
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Installation of r2excel package
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updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 10
46,729 results • Page 230 of 935
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Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
It is fine for your mass spec facility to include blank samples as part of their internal QC, but such samples should not in my opinion be …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Hm, okay, in building a fake model by hand I think I'm realizing the problem: `mouse` and its variants are ideally acting as basically a ra…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Ah, this is handy! Hopefully this will help with troubleshooting; at the very least, I can see it being helpful when I try to explain to pe…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You may want to look at the coefficients you are trying to estimate with ExploreModelMatrix: https://www.bioconductor.org/packages/relea…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by emily.wolfrum • 0
Hi Gordon, Thanks for the quick reply. The technical or process blank samples I'm referring to are part of a set of quality control sampl…
Votes
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
Answer: When to use edgeR or limma
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