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Showing :
microarray
•
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0
votes
1
reply
27
views
affy::rma results doesn't match with ncbi website
affy
Preprocessing
Microarray
updated 31 minutes ago by
ATpoint
★ 4.7k • written 11 hours ago by
akp9132
• 0
1
vote
8
replies
1.6k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 4 months ago by
Adam Marstrand
• 0
0
votes
1
reply
208
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
updated 7 weeks ago by
ATpoint
★ 4.7k • written 7 weeks ago by
Reuben
• 0
17
votes
8
replies
11k
views
remove microarray batch effects using Limma
Microarray
updated 8 months ago by
Gordon Smyth
52k • written 14.4 years ago by
Xie, Zhi NIH/NHLBI [E]
▴ 120
2
votes
2
replies
1.3k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 10 months ago by
XW
• 0 • written 8.8 years ago by
tati6406
• 0
5
votes
8
replies
10k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 10 months ago by
hortense96
• 0 • written 8.6 years ago by
dmcleanuk
▴ 30
1
vote
5
replies
2.5k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 10.1 years ago by
chandlerjd58
▴ 10
2
votes
2
replies
3.8k
views
Biostatistician Position: UMass Medical School
Microarray
Microarray
written 17.7 years ago by
David Lapointe
▴ 190
1
vote
4
replies
4.8k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 2.3 years ago by
Sarah
• 0
11
votes
4
replies
2.4k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 17 months ago by
Gordon Smyth
52k • written 6.1 years ago by
tleona3
• 0
1
vote
6
replies
2.6k
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 19 months ago by
Gordon Smyth
52k • written 4.5 years ago by
linouhao
▴ 20
0
votes
2
replies
1.6k
views
Calculation of t-tests for factorial design
Microarray
limma
Microarray
limma
written 14.5 years ago by
Pascal Gellert
▴ 80
0
votes
2
replies
1.1k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray
Alignment
Biostrings
written 22 months ago by
sandmann.t
▴ 70
0
votes
7
replies
1.6k
views
A question about Limma
PROcess
Microarray
limma
20.2 years ago • updated 22 months ago
Gordon Smyth
52k
1
vote
2
replies
1.4k
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
23 months ago
Abdul
▴ 20
2
votes
2
replies
984
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
23 months ago
Abdul
▴ 20
0
votes
2
replies
1.1k
views
Full list of differential genes not obtained in topTable
Microarray
GEOquery
topTable
limma
updated 23 months ago by
Gordon Smyth
52k • written 23 months ago by
Ankita
• 0
2
votes
2
replies
1.1k
views
Question about avereps function of limma
avereps
probes
average
limma
Microarray
updated 2.0 years ago by
Gordon Smyth
52k • written 2.0 years ago by
mohammedtoufiq91
▴ 10
0
votes
0
replies
911
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
2.1 years ago
agamemnon
• 0
7
votes
1
reply
16k
views
ERROR: No residual degrees of freedom in linear model fits
Microarray
updated 2.1 years ago by
yr542
• 0 • written 10.9 years ago by
jesus urbano
▴ 40
1
vote
6
replies
3.2k
views
TCGA: clinical data and expression data
microarray
annotation
cancer
updated 2.1 years ago by
Sharif
• 0 • written 4.5 years ago by
641549298
• 0
0
votes
17
replies
3.3k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 2.1 years ago by
Gordon Smyth
52k • written 2.4 years ago by
Sam
• 0
0
votes
1
reply
923
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
Aleksandra
• 0
0
votes
2
replies
1.4k
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
2.2 years ago
dqt
• 0
0
votes
2
replies
970
views
Celfiles not reading in
Microarray
written 2.2 years ago by
Oluwaseun
• 0
2
votes
6
replies
4.7k
views
Convert Chromosome postions to hgnc_symbol using R
microarray
updated 2.3 years ago by
mbansal
• 0 • written 5.3 years ago by
joyk2a
• 0
3
votes
2
replies
8.0k
views
How to convert Illumina HT_12_v4 annotation
convert
R
annotation
microarray
illumina human ht-12 v4
updated 2.3 years ago by
snijesh
▴ 200 • written 7.3 years ago by
p_donchev84
• 0
6
votes
6
replies
1.8k
views
Too many differentially expressed miRNA with limma
limma
miRNA
Microarray
2.3 years ago
Sara
▴ 20
5
votes
2
replies
3.1k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray
limma
DifferentialExpression
updated 2.6 years ago by
Gordon Smyth
52k • written 3.6 years ago by
Nikshay
▴ 10
0
votes
1
reply
984
views
Compare different cell lines with tissues using limma
limma
MicroarrayData
Microarray
Agilent
updated 2.7 years ago by
Gordon Smyth
52k • written 2.7 years ago by
Sam
• 0
0
votes
8
replies
1.9k
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
2.7 years ago
YC
• 0
2
votes
13
replies
5.3k
views
Error in using r
microarray
updated 2.8 years ago by
17545106088
• 0 • written 8.4 years ago by
azhar
• 0
0
votes
4
replies
1.4k
views
Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray
DifferentialExpression
2.8 years ago
S
• 0
1
vote
2
replies
1.1k
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
2.8 years ago
Mikołaj Mierzejewski
• 0
1
vote
2
replies
1.5k
views
Affymetrix analysis of microarray by using Limma
limma
MicroarrayData
Microarray
Affymetrix
2.8 years ago
Mikołaj Mierzejewski
• 0
4
votes
10
replies
2.5k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219
Microarray
oligo
AffymetrixChip
2.8 years ago
Yang Shi
▴ 10
3
votes
4
replies
2.3k
views
Quantile Normalization after rma or not?
limma
Microarray
oligo
2.8 years ago
Yang Shi
▴ 10
2
votes
2
replies
1.1k
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db
Microarray
oligo
2.8 years ago
Yang Shi
▴ 10
2
votes
5
replies
3.1k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi
Microarray
2.9 years ago
nhaus
▴ 70
0
votes
2
replies
1.1k
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db
MicroarrayData
Microarray
pd.clariom.d.human
2.9 years ago
amir.rakhimov.b
• 0
5
votes
11
replies
5.8k
views
Duplicate gene ID's returned from limma microarray analysis
limma
microarray
updated 2.9 years ago by
Gordon Smyth
52k • written 8.2 years ago by
mat149
▴ 80
1
vote
2
replies
1.9k
views
Time course experiment using limma
limma
Multi-levelExperiments
Microarray
2.9 years ago
Wendy
▴ 10
0
votes
12
replies
2.1k
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
2.9 years ago
Adam
• 0
1
vote
7
replies
9.3k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray
normalization
oligo HTA
updated 3.0 years ago by
Harald
• 0 • written 6.2 years ago by
RV
▴ 10
0
votes
0
replies
876
views
Error in svd(X) when using edge lrt (or odp) function.
edge
Microarray
longitudinal
3.0 years ago
emily
• 0
2
votes
5
replies
2.3k
views
Adjust for base line gene expression in limma model
limma
Microarray
updated 3.2 years ago by
Gordon Smyth
52k • written 3.2 years ago by
S
• 0
4
votes
6
replies
1.7k
views
RMA on different disease labels
rma
background
microarray
normalization
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
Joshua
• 0
1
vote
1
reply
1.6k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
Caitlin
▴ 50
0
votes
1
reply
1.5k
views
Re-normalize microarray dataset in R
microarray
quantile
expression
R
Normalization
updated 3.7 years ago by
Konstantinos Yeles
▴ 80 • written 3.7 years ago by
mohammedtoufiq91
▴ 10
3
votes
5
replies
2.2k
views
Use of arrayWeights with two treatment groups
Microarray
arrays
limma
MicroarrayData
updated 3.7 years ago by
Gordon Smyth
52k • written 3.8 years ago by
Emma
• 0
50 results • Page
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Answer: affy::rma results doesn't match with ncbi website
by
ATpoint
★ 4.7k
Exact OMCIS reproduction down to the values without code and software version is borderline impossible. Either use the values as provided o…
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by
James W. MacDonald
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You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column
by
Erika
• 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping
by
James W. MacDonald
68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question?
by
DavideSant
• 0
Thank you, this was super useful!
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
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