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error
•
reset
0
votes
7
replies
1.5k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error
RStudio
ggplot2
DESeq2
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
BioES
• 0
10
votes
10
replies
6.7k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 5 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
0
votes
0
replies
276
views
proActiv - Error in estimateSizeFactorsForMatrix when using the proActiv function
proActiv
error
estimateSizeFactorsForMatrix
6 months ago
Chris
• 0
0
votes
1
reply
385
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
6 months ago
leon
• 0
0
votes
3
replies
611
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
jason.kost
• 0
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 10 months ago by
snow34
• 0 • written 6.6 years ago by
ap3637
• 0
0
votes
1
reply
463
views
Calculate RPKMs and Output proteins pass the cutoff into FASTA file ... Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse") : i…
customProDB
easyrun
error
mm10
Mus_musculus_Data
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Esraa
• 0
0
votes
0
replies
478
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
12 months ago
aymanreffai
• 0
0
votes
8
replies
1.1k
views
fail to annotate chromosome data to single cell object
error
SingleCell
annotate
updated 5 months ago by
yw24418
• 0 • written 13 months ago by
sandra.garces.19
• 0
0
votes
2
replies
541
views
Error message trying to open downloaded package
error
DEP
14 months ago
kcpaul168
• 0
0
votes
0
replies
540
views
DEqMS function "outputResult" reports wrong sca.adj.pval
outputresult
DEqMS
sca.adj.pval
error
p-value
18 months ago
Bastian
• 0
0
votes
3
replies
962
views
tximport error
error
tximport
updated 19 months ago by
Michael Love
41k • written 19 months ago by
hana
• 0
0
votes
3
replies
2.1k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet
Assay
NanoString
Error
Data
updated 21 months ago by
James W. MacDonald
65k • written 21 months ago by
junli1988
• 0
0
votes
7
replies
1.4k
views
Centos 7.8, custom-compiled R-4.1: iPath_1.0.0 won't install
error
iPath
R
compilation
2.3 years ago
wjb2130
• 0
0
votes
2
replies
818
views
Error in TFBSTools at SitesetList
error
TFBSTools
R
2.5 years ago
HELEN
• 0
4
votes
9
replies
3.7k
views
biomaRt - getBM; Error with obtaining a dataset from getBM() function
biomaRt
error
getBM
updated 2.9 years ago by
Mike Smith
★ 6.5k • written 3.2 years ago by
Zen
▴ 20
0
votes
3
replies
877
views
bioconductor.org not reachable from EU region
error
http429
server
3.0 years ago
ashu.upadhyay2206
• 0
0
votes
2
replies
1.3k
views
Finding the correct version of DESeq2 for my version of R (3.6.1)
error
DESeq2
Install
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
Mick
• 0
1
vote
2
replies
2.9k
views
error in DESeq2 results(dds)
DESeq2
datasetfrommatrix
results
error
3.2 years ago
james
• 0
3
votes
4
replies
2.9k
views
R Error: package ‘GenomeInfoDb’ could not be loaded on MacBook
error
mac
DESeq2
GenomeInfoDb
R
3.3 years ago • updated 3.2 years ago
Dan
▴ 20
1
vote
1
reply
961
views
Errors in installing RforProteomics package
error
RforProteomics
Install
updated 3.4 years ago by
Mike Smith
★ 6.5k • written 3.4 years ago by
Phoebe
• 0
0
votes
1
reply
723
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
3.8 years ago
akhaira
• 0
6
votes
6
replies
1.2k
views
Suggestion for next revision of edgeR User Guide re Design matrix setup
edger
error
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
pdunn
• 0
0
votes
14
replies
2.2k
views
annFUN error TOPGO
TOPGO
annFUN
error
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
eleonora.porcu
• 0
0
votes
0
replies
585
views
Error on FindOptimalBinning function
bhc
error
4.1 years ago
pavel.granalacant
• 0
0
votes
0
replies
842
views
Multicollinearity and pR2Y =0.1
opls-da
error
multicollinearity
4.2 years ago
adriana.roca-fernandez
• 0
0
votes
1
reply
994
views
boxplot Error in Bioconductor
boxplot
bioconductor
R
error
4.3 years ago
l154359
• 0
0
votes
4
replies
956
views
nucleR ERROR unable to find an inherited method for function peakDetection for signature
nucleosome
peaks
error
Job
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
anne.kannengiesser
• 0
0
votes
5
replies
1.5k
views
readTranscriptFeatures from genomation
R
Rstudio
Error
readTranscriptFeatures
genomation
updated 4.4 years ago by
altuna akalin
▴ 20 • written 4.4 years ago by
hwaterma
• 0
0
votes
3
replies
797
views
Error in E-Eb Limma package
limma
error
E-Eb
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
diego.orihuelatacuri
• 0
4
votes
7
replies
1.2k
views
bam files to hilbert curve
HilbertCurve
error
bamfiles
GRobject
4.6 years ago
adklts
• 0
0
votes
6
replies
7.9k
views
Rhtslib - install error
Rhtslib
installation
error
zlib
updated 4.6 years ago by
leoadam014
• 0 • written 5.5 years ago by
boboshaq
• 0
0
votes
1
reply
1.3k
views
DiffBind dba error
DiffBind
dba
R
error
updated 4.7 years ago by
Rory Stark
★ 5.2k • written 4.9 years ago by
annika-helverson
• 0
0
votes
1
reply
1.2k
views
Help with installation of readat package
readat
error
updated 4.7 years ago by
shepherl
3.8k • written 4.7 years ago by
tbryson1
• 0
2
votes
2
replies
1.5k
views
TCGAbiolinks GDCprepare error
TCGAbiolinks
GDCprepare
error
updated 4.8 years ago by
Tiago C. Silva
▴ 270 • written 4.8 years ago by
Talip Zengin
▴ 10
0
votes
1
reply
1.7k
views
R: oligo packages install error
oligo
packages
error
updated 4.8 years ago by
Martin Morgan
25k • written 4.8 years ago by
get3232
• 0
0
votes
0
replies
828
views
Error in parseGenBank
genbankr
parseGenBank
gbk
error
4.8 years ago
ashley.dederich
• 0
2
votes
3
replies
996
views
How can I overcome the error of "No residual degrees of freedom in linear model fits"?
limma
microarray
error
updated 4.8 years ago by
Dario Strbenac
★ 1.5k • written 4.8 years ago by
Jurat Shahidin
▴ 80
0
votes
6
replies
4.1k
views
Error in getOneSeqFromBSgenomeMultipleSequences During singeR tutorial
error
4.8 years ago
dfcarril
• 0
0
votes
4
replies
1.9k
views
DESeq2 compare all_vs_all levels error
deseq2
error
RNAseq
updated 4.8 years ago by
swbarnes2
★ 1.3k • written 4.8 years ago by
aishu.jp
▴ 30
0
votes
3
replies
956
views
Error in if (all(x <= minReadCount) & lambda <= minReadCount) { : missing value where TRUE/FALSE needed
cnmops
cn.mops
error
updated 4.9 years ago by
Martin Morgan
25k • written 4.9 years ago by
s1812756
• 0
0
votes
6
replies
1.9k
views
atacseqQC error while splittin the bamfile
ATACseqQC
ATAC-seq
error
split bam file
updated 5.0 years ago by
contact
• 0 • written 5.0 years ago by
Theo
▴ 10
0
votes
8
replies
2.5k
views
tximport command error
tx2gene
txi
error
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
eliztran
• 0
2
votes
6
replies
1.5k
views
EdgeR glmTreat error
edger
error
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
lucap
• 0
1
vote
1
reply
1.0k
views
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1
biomaRt
error
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
steppydeklin
▴ 10
0
votes
1
reply
797
views
Error in intramodularConnectivity(ADJ1, colorh1) : object 'colorh1' not found
error
wgcna
affymetrix data
updated 5.1 years ago by
Peter Langfelder
★ 3.0k • written 5.1 years ago by
pratikshasharma47
• 0
2
votes
6
replies
1.9k
views
featurecounts Rsubread ERROR on exon_id
R
error
software error
Rsubread
featurecounts
updated 5.1 years ago by
Wei Shi
★ 3.6k • written 5.1 years ago by
edejong
• 0
2
votes
3
replies
3.2k
views
DESeq2- preliminary study no replicates
deseq2
replicates
error
DESeqDataSetFromMatrix
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
Yonatan Amzaleg
• 0
1
vote
1
reply
1.1k
views
Error in getBM(c("affy_rice", "ensembl_gene_id", "entrezgene", "external_gene_name"), : could not find function "featureNames"
annotation
error
biomaRT
affy
ricedataset
updated 5.1 years ago by
Mike Smith
★ 6.5k • written 5.1 years ago by
pratikshasharma47
• 0
1
vote
2
replies
2.0k
views
Errors installing mzR package
proteomics
error
updated 5.1 years ago by
Laurent Gatto
1.6k • written 5.1 years ago by
pdaltron
• 0
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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