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Views
Votes
1
vote
0
replies
3.7k
views
Batch effect confounded with additional covariate
9.8 years ago
Guest User
★ 13k
1
vote
4
replies
3.7k
views
Issue with qvalue function: Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are not allowed
qvalue
4.7 years ago
anamaria
▴ 10
0
votes
3
replies
3.7k
views
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
Martin Morgan
25k • written 5.2 years ago by
venkatarao142152
• 0
3
votes
11
replies
3.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.1 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
0
votes
2
replies
3.6k
views
Error in UseMethod("rescale")
clusterProfiler
updated 17 months ago by
Guido Hooiveld
★ 4.0k • written 17 months ago by
vvelagal
• 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
0
replies
3.6k
views
rhdf5::h5dump requires write access
rhdf5
9.6 years ago
friedmab
▴ 10
0
votes
2
replies
3.6k
views
R Version 3.6.1
software error
Tutorial
updated 4.8 years ago by
Laurent Gatto
1.6k • written 4.8 years ago by
naeemurself
• 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
views
RNA-seq Differential expression using 3 groups
rnaseq
anova
deseq2
edger
genespring
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
views
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
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
andresrabinovich
• 0 • written 19 months ago by
thithusuong.nguyen
• 0
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
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
6
replies
3.4k
views
Merge problems in R
methylationArrayAnalysis
ChAMP
MethylationArrayData
2.8 years ago
FWNL15
• 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
2
votes
2
replies
3.4k
views
problem using AnnotationDbi
annotationdbi
bioconductor
6.3 years ago
h72ghorashi
• 0
0
votes
2
replies
3.4k
views
DEXSeq on FeatureCounts output
dexseq
featurecounts
8.7 years ago
Vivek.b
▴ 100
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
views
Secure Account Update
15.5 years ago
Abbey National Plc.
▴ 10
0
votes
0
replies
3.4k
views
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
views
Retrieving genes by their genome locations in biomart
biomaRt
biomaRt
16.1 years ago
Steffen
▴ 500
0
votes
0
replies
3.4k
views
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
6.0 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?
Mus musculus
biomaRt
ChIPpeakAnno
Mus musculus
biomaRt
ChIPpeakAnno
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
views
KEGG Pathway in R
keggrespathways
KEGG
updated 23 months ago by
Kevin Blighe
★ 3.9k • written 23 months ago by
salethlr
• 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
14.9 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
3.3k
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
Kevin Blighe
★ 3.9k • written 2.8 years ago by
yura.grabovska
▴ 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
Michael Love
42k • written 18 months ago by
Rob
• 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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Replies
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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