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Job:
Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod
Evolution
QuantitativeTrailLocus
Genetics
JobPosting
40 minutes ago
pierre.devillemereuil
• 0
0
votes
1
reply
35
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
curl
microRNA
starBase
webapi
ENCORI
updated 4 hours ago by
ATpoint
★ 4.1k • written 5 hours ago by
V_Vibes
• 0
0
votes
1
reply
31
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 31 minutes ago by
James W. MacDonald
65k • written 6 hours ago by
Đình Vinh
• 0
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
6 hours ago
shahrozimmac
0
0
votes
1
reply
37
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 30 minutes ago by
James W. MacDonald
65k • written 8 hours ago by
ttt
• 0
0
votes
0
replies
22
views
Processing of curatedmetagenomics
curatedMetagenomicData
12 hours ago
Edward
• 0
0
votes
1
reply
30
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 20 minutes ago by
James W. MacDonald
65k • written 20 hours ago by
boczniak767
▴ 720
0
votes
1
reply
35
views
How to run allelic imbalance in apeglm
apeglm
20 hours ago • updated 4 hours ago
euge.eugenio
▴ 20
0
votes
0
replies
31
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
1 day ago
Bibi
• 0
0
votes
5
replies
133
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
1 day ago • updated 2 hours ago
Galina
• 0
1
vote
2
replies
80
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 1 hour ago
Anna
• 0
0
votes
0
replies
39
views
ERROR; return code from pthread_create() is 22
affy
2 days ago • updated 1 day ago
pickingastar
• 0
0
votes
0
replies
43
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
2 days ago • updated 1 day ago
Abiologist
• 0
0
votes
2
replies
126
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 2 days ago by
Michael Love
42k • written 2 days ago by
shaunpeterson
• 0
0
votes
3
replies
112
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 2 days ago by
damian.szk
▴ 80 • written 3 days ago by
ninidea
• 0
0
votes
5
replies
506
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 1 hour ago by
Michael Love
42k • written 3 days ago by
Ken C
• 0
0
votes
2
replies
116
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
3 days ago
makala
• 0
0
votes
0
replies
55
views
determine k during RUVSeq
RUVSeq
RUVnormalize
4 days ago
Ειρήνη
• 0
0
votes
0
replies
55
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
4 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
15
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
4 days ago
oliverelijhan
0
0
votes
0
replies
83
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
4 days ago
Anton01
• 0
2
votes
3
replies
120
views
Problem installing ChAMP on a MacBook
ChAMP
updated 4 days ago by
shepherl
3.9k • written 4 days ago by
Galia
• 0
0
votes
0
replies
48
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
4 days ago
danalvoronov
▴ 10
0
votes
0
replies
48
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
4 days ago
k200987
• 0
2
votes
5
replies
224
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
4 days ago • updated 3 days ago
Patadù
▴ 10
0
votes
4
replies
140
views
error running enricher from clusterprofiler
clusterProfiler
cluster
5 days ago • updated 4 days ago
Yael
• 0
2
votes
3
replies
132
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 5 days ago by
Guillermo
• 0
0
votes
0
replies
44
views
Difference in Contrast in DiffBind
DiffBind
5 days ago
zzrammal
• 0
4
votes
9
replies
266
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 4 days ago by
ATpoint
★ 4.1k • written 5 days ago by
pangtaihin
• 0
1
vote
2
replies
104
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
5 days ago
Patadù
▴ 10
0
votes
3
replies
124
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 5 days ago by
Michael Love
42k • written 5 days ago by
Kasper
• 0
1
vote
2
replies
135
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
5 days ago • updated 4 days ago
Daniel
• 0
1
vote
0
replies
69
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
6 days ago
Aleena
▴ 30
0
votes
0
replies
61
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
6 days ago
Researcher
• 0
1
vote
3
replies
256
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Ashley
• 0
1
vote
2
replies
251
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
6 days ago • updated 3 days ago
BioinfGuru
▴ 30
0
votes
8
replies
514
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 5 days ago by
BioinfGuru
▴ 30 • written 6 days ago by
Eric Katagirya
• 0
0
votes
1
reply
102
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 5 days ago by
Michael Love
42k • written 6 days ago by
piemmea
• 0
0
votes
2
replies
109
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
7 days ago • updated 5 days ago
Yveto
• 0
2
votes
1
reply
82
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 5 days ago by
Alejandro Reyes
★ 1.9k • written 7 days ago by
Sara
• 0
0
votes
3
replies
190
views
ChAMP installation issue
Cha
ChAMP
7 days ago • updated 6 days ago
e1271094
• 0
0
votes
1
reply
152
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 7 days ago by
Guido Hooiveld
★ 4.0k • written 7 days ago by
aogunbaw
• 0
0
votes
2
replies
141
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 5 days ago by
zhouwanding
▴ 10 • written 8 days ago by
Seungmin
• 0
2
votes
2
replies
397
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
8 days ago • updated 3 days ago
Matthew Thornton
▴ 360
0
votes
1
reply
180
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
sajadahmad41454
• 0
0
votes
0
replies
85
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
10 days ago
neilzhao
▴ 30
0
votes
1
reply
114
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 11 days ago by
ATpoint
★ 4.1k • written 11 days ago by
sajadahmad41454
• 0
1
vote
2
replies
282
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
11 days ago • updated 10 days ago
Dylan.Sheerin
• 0
2
votes
7
replies
410
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
12 days ago • updated 9 days ago
sajadahmad41454
• 0
0
votes
0
replies
77
views
Treeio as.treedata function seq lenght error
treeio
12 days ago
nromerov
• 0
170 results • Page
1 of 4
Recent ...
Replies
Answer: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
by
James W. MacDonald
65k
It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
Answer: Control group between 2 batches have different expression in RNAseq data
by
James W. MacDonald
65k
Since batch is orthogonal to the treatment, you just add a batch factor to your model.
Answer: Subsetting RNAseq data | voomaByGroup()
by
Anna
• 0
Hi Gordon. Thank you so much. Your reply is extremely helpful, and I feel more confident moving forward with the analysis. Also, very inte…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
edgeR used a prior count which stabilizes LFC while DESeq2 does not. Note that the SE are larger in these cases so you don't have experime…
Votes
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
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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