1
vote
0
replies
3.7k
views
Batch effect confounded with additional covariate
9.8 years ago Guest User ★ 13k
0
votes
1
reply
3.7k
views
ape - delete bootstrap values (node.labels) less than a certain value
ape bootstrap node phylogenetic tree
8.9 years ago wd ▴ 30
0
votes
3
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3.7k
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Problem with gcc/fortran compilers in new version of Bioconductor (Mac M1)
biocmanager R gofortran Bioconductor
2.0 years ago Olivia • 0
0
votes
1
reply
3.6k
views
getGEO Failed to connect to ftp.ncbi.nlm.nih.gov port 21: Timed out
getGEO
8.3 years ago maedakus ▴ 10
0
votes
2
replies
3.6k
views
Web Scraping From Pubmd (I want to extract gene articles form pubmed abstract and pubmed id i want to extract for number of genes)
cancer gene
updated 5.2 years ago by 25k • written 5.2 years ago by • 0
3
votes
11
replies
3.6k
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The low successful assignment ratio of FeatureCounts
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2.1 years ago • updated 2.0 years ago Sarah_piggy ▴ 10
0
votes
1
reply
3.6k
views
cannot : source("https://bioconductor.org/biocLite.R")
software error
7.4 years ago kc9qey • 0
1
vote
2
replies
3.6k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
4.1 years ago chatterjee.arumoy ▴ 10
0
votes
2
replies
3.6k
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Error in UseMethod("rescale")
clusterProfiler
updated 17 months ago by ★ 4.0k • written 17 months ago by • 0
0
votes
0
replies
3.6k
views
rhdf5::h5dump requires write access
rhdf5
9.6 years ago friedmab ▴ 10
0
votes
2
replies
3.6k
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R Version 3.6.1
software error Tutorial
updated 4.8 years ago by 1.6k • written 4.8 years ago by • 0
0
votes
0
replies
3.6k
views
Inquiries about fitType on DESeq2
Regression DESeq2 Regression DESeq2
10.5 years ago Michael Love 42k
2
votes
1
reply
3.5k
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RNA-seq Differential expression using 3 groups
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8.8 years ago BM • 0
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.1 years ago stats134711 • 0
1
vote
4
replies
3.5k
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Looking for Batch effects in PCA
batch effect pca
5.9 years ago • updated 16 months ago KB ▴ 50
0
votes
2
replies
3.5k
views
minfi::read.metharray.exp error ("The following specified files do not exist")
minfi read.metharray.exp
7.6 years ago supermanrocketboy ▴ 10
4
votes
2
replies
3.4k
views
Difference between "be" and "leek" methods when deciding number of surrogate variables to estimate with SVA?
sva num.sv
6.9 years ago brhead ▴ 40
0
votes
1
reply
3.4k
views
"Package which is only available in source form, and may need compilation of C/C++/Fortran"
networkBMA error
6.8 years ago milenamagalhaes • 0
0
votes
6
replies
3.4k
views
Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
2.8 years ago FWNL15 • 0
0
votes
0
replies
3.4k
views
maQualityPlots: cannot coerce type 'S4' to vector of type 'double'
arrayQuality arrayQuality
10.3 years ago Saket Choudhary ▴ 130
0
votes
3
replies
3.4k
views
ASpli: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'sort': 'start' or 'end' canno…
ASpli
updated 8 months ago by • 0 • written 19 months ago by • 0
0
votes
3
replies
3.4k
views
Unable to reroot RAxML tree with ggtree
ggtree raxml reroot tree
6.3 years ago kevin.liam.keegan • 0
0
votes
2
replies
3.4k
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DEXSeq on FeatureCounts output
dexseq featurecounts
8.7 years ago Vivek.b ▴ 100
2
votes
2
replies
3.4k
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problem using AnnotationDbi
annotationdbi bioconductor
6.3 years ago h72ghorashi • 0
0
votes
0
replies
3.4k
views
ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: system is exactly singular: U[4, 4] = 0
Normalization Clustering affy Normalization Clustering affy
10.1 years ago Guan ▴ 20
1
vote
4
replies
3.4k
views
GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
affymetrixchip GenechipHumanTranscriptomeArray2.0 exon array analysis
9.2 years ago svlachavas ▴ 830
0
votes
0
replies
3.4k
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Secure Account Update
15.5 years ago Abbey National Plc. ▴ 10
0
votes
0
replies
3.4k
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Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.3 years ago Elena Serrano ▴ 30
0
votes
0
replies
3.4k
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Retrieving genes by their genome locations in biomart
biomaRt biomaRt
16.1 years ago Steffen ▴ 500
0
votes
0
replies
3.4k
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LIMMA - No residual degrees of freedom in linear model fits
limma limma
19.0 years ago Gordon Smyth 50k
0
votes
8
replies
3.4k
views
featureCounts Returns 0.0% successfully assigned fragments
rsubread featurecounts
5.9 years ago connor.geraghty • 0
0
votes
0
replies
3.4k
views
Error: : Error in dim(data) <- dim : attempt to set an attribute on NULL
limma limma
15.3 years ago Sally ▴ 250
0
votes
4
replies
3.4k
views
[Solved]Preserve metadata column for retrieving common regions from two GRanges objects
granges intersect
8.2 years ago Jurat Shahidin ▴ 80
0
votes
0
replies
3.4k
views
build TSS from biomaRt for ChIPpeakAnno, how to decide the mm9 and mm10 assembly?
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11.2 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
3.3k
views
an error in ggbio: "Breaks and labels are different lengths"
ggbio ggplot2
7.1 years ago Bogdan ▴ 670
0
votes
2
replies
3.3k
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KEGG Pathway in R
keggrespathways KEGG
updated 23 months ago by ★ 3.9k • written 23 months ago by • 0
2
votes
4
replies
3.3k
views
I want to make a geneList for clusterProfiler analysis but I get "error in do.call( cbind lapply(x is.na )) variable names are limited to 10000 bytes"
clusterProfiler
3.4 years ago Emilia ▴ 30
3
votes
3
replies
3.3k
views
Modifying or writing a FCS file in R using the FlowCore package
FCS flowframe flowcore flow cytometry
5.7 years ago vonskopnik ▴ 10
1
vote
0
replies
3.3k
views
Calculating average expression value in limma topTable output
probe probe
13.5 years ago Sunny Srivastava ▴ 350
0
votes
2
replies
3.3k
views
CPM function in EDGER
edger cpm rnaseq
3.7 years ago francesca3 • 0
0
votes
2
replies
3.3k
views
Pipeline for analyzing CNV (SNP array) level 3 from TCGA
SNP CNV TCGA
9.1 years ago NS ▴ 60
0
votes
0
replies
3.3k
views
Urgent..........Problem in using ABarray
ABarray ABarray
14.8 years ago Priyanka Jain ▴ 20
0
votes
1
reply
3.3k
views
Error: vector memory exhausted (limit reached?)
software error
5.9 years ago mdroog • 0
1
vote
8
replies
3.2k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
2.6 years ago • updated 2.5 years ago v.merino.nicolas ▴ 10
0
votes
3
replies
3.2k
views
How to count barcode sequences in a fastq file
fastq barcoding
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by ▴ 30
0
votes
0
replies
3.2k
views
lumi export
lumi lumi
14.6 years ago Mervi Alanne ▴ 70
0
votes
0
replies
3.2k
views
edgeR: Specifying the "coef"-argument in glmLRT in a two factor study
edgeR edgeR
12.1 years ago Gordon Smyth 50k
0
votes
7
replies
3.2k
views
Mouse GSEA Analysis
clusterProfiler
updated 17 months ago by 42k • written 18 months ago by • 0
0
votes
0
replies
3.2k
views
Pathview+GAGE workflow on RNA-seq data pathway analysis and visualization (was: Pathview published in Bioinformatics)
Annotation Pathways Visualization graph PROcess gage pathview Annotation Pathways graph
10.8 years ago Luo Weijun ★ 1.6k
0
votes
16
replies
3.2k
views
Rgraphviz installation fails
rgraphviz
6.8 years ago Giovanni Calice ▴ 160
1,000 results • Page 3 of 20
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Answer: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
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