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33
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
1 day ago Chris • 0
0
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0
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63
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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools TCGA
5 days ago glaciya2018 • 0
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how to do Differential splicing from SGSeq analysis
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6 days ago • updated 1 day ago Sara • 0
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Exon-exon Junction Analysis for Variable-length Exons
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6 days ago Dario Strbenac ★ 1.5k
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8
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308
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DESeq2 output used for PCA plot on R studio
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updated 5 days ago by ★ 1.3k • written 7 days ago by • 0
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2
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207
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featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
7 days ago • updated 5 days ago shuwangxinze1996 • 0
1
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13
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351
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Trying to use enrichGO
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9 days ago • updated 6 days ago fernanda.backsouza ▴ 10
0
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Unlocking Potential: NURS FPX Strategies and Insights
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9 days ago vaxahey107 • 0
0
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0
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85
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I am trying to detect alternative splicing.
ASpli
10 days ago Sebashish • 0
0
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0
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105
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Warning while loading DEP package
DEP
updated 12 days ago by 3.8k • written 12 days ago by • 0
1
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2
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197
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significant difference of p-values with dream() after updating VariancePartition
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12 days ago Le • 0
1
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2
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140
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Error in champ.load(): The following specified files do not exist
ChAMP
13 days ago • updated 12 days ago Sherin • 0
0
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1
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89
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Input Question for deseq.r
RSeqAn
updated 12 days ago by ★ 4.1k • written 13 days ago by • 0
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4
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210
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
13 days ago • updated 10 days ago lonn • 0
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Enzyme Engineering
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13 days ago bocchemistry • 0
0
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0
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84
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Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror IsoCorrectoR
14 days ago Maliha Tabassum • 0
0
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1
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109
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what is the sampleFiles
chipseq
updated 14 days ago by 65k • written 14 days ago by • 0
0
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0
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84
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Diffbind Error in socketConnection
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15 days ago Virangika • 0
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0
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[ChIPseeker] Unable to perform gene ontology analysis
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15 days ago Henry ▴ 10
0
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1
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119
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Deseq2 Rlog transformation
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updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
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[DiffBind] Obtaining normalization factors
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18 days ago • updated 14 days ago Henry ▴ 10
0
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3
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A ComBat-seq issue: the covariates are confounded
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updated 12 days ago by ▴ 850 • written 18 days ago by • 0
0
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0
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Cannot use `readVcf()` on a file created with `writeVcf()`
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18 days ago Stevie Pederson • 0
3
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6
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257
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
19 days ago nhaus ▴ 30
0
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1
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164
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DESeq2 gives an error and R crashes
DESeq2
19 days ago • updated 18 days ago Shefali • 0
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0
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120
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LearnTaxa with custom Silva
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20 days ago Eryn • 0
0
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0
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80
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queryDGIdb lexical error for some genes
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20 days ago Dennis • 0
0
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1
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145
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compareCluster dotplot: how to modify the genesets order
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updated 16 days ago by ★ 3.9k • written 20 days ago by • 0
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0
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102
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ggtree tip label position (depth)
ggtree
21 days ago • updated 20 days ago Roope • 0
2
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6
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372
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How to make boxplot with pairwise and overall p value from Limma
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22 days ago Chris • 0
0
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0
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136
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
25 days ago andromeda • 0
0
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1
reply
120
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Granges regionCounts not returning the expected number of entries
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25 days ago Modoc Kesner ▴ 10
0
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0
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flowDensity on a flowset
flowDensity
26 days ago fredrikwallberg • 0
0
votes
0
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82
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DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
26 days ago Macsue • 0
0
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1
reply
148
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 28 days ago by 65k • written 29 days ago by • 0
0
votes
2
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282
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Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
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4 weeks ago • updated 25 days ago fer_talavera • 0
0
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2
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244
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
4 weeks ago • updated 11 days ago isaac.vock • 0
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7
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365
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Internet connection for Bioconductor packages in Rstudio in Iran...
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4 weeks ago • updated 28 days ago needNGS • 0
0
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0
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104
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How to extract the coordinate of dba.plotPCA?
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4 weeks ago feather-W • 0
0
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0
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103
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PCA plot for normalized counts using Diffbind
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4 weeks ago Ankit ▴ 20
1
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5
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326
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fgsea fork
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updated 4 weeks ago by 65k • written 4 weeks ago by • 0
0
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0
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89
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
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4 weeks ago Pierre Lindenbaum ▴ 10
3
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3
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379
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Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 5 weeks ago by ▴ 160 • written 5 weeks ago by • 0
0
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0
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111
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
5 weeks ago gshweta95 • 0
2
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1
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200
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Only positive enrichment score in GSEA
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updated 5 weeks ago by ★ 3.9k • written 5 weeks ago by ▴ 10
0
votes
0
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111
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Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
5 weeks ago nromerov • 0
1
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3
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254
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cBioPortalData loads empty z-score expression table
cBioPortalData
updated 5 weeks ago by 690 • written 5 weeks ago by • 0
0
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0
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122
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crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray cdf crlmm
5 weeks ago mayra.haedo • 0
0
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0
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109
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Macsquant FCS in read.FCS & opencyto
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5 weeks ago taylor.witte • 0
0
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0
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131
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Multifactor analysis in DiffBind
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5 weeks ago erbrocato • 0
392 results • Page 1 of 8
Recent ...
Replies
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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