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Showing :
microarray
•
reset
0
votes
2
replies
713
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray
Alignment
Biostrings
written 12 months ago by
sandmann.t
▴ 70
1
vote
2
replies
902
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
13 months ago
Abdul
▴ 20
2
votes
2
replies
674
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
13 months ago
Abdul
▴ 20
0
votes
2
replies
694
views
Full list of differential genes not obtained in topTable
Microarray
GEOquery
topTable
limma
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Ankita
• 0
2
votes
2
replies
659
views
Question about avereps function of limma
avereps
probes
average
limma
Microarray
updated 14 months ago by
Gordon Smyth
50k • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
0
replies
625
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
14 months ago
jsharif
• 0
0
votes
1
reply
638
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
Aleksandra
• 0
0
votes
2
replies
937
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
16 months ago
dqt
• 0
0
votes
2
replies
718
views
Celfiles not reading in
Microarray
written 16 months ago by
Oluwaseun
• 0
6
votes
6
replies
1.4k
views
Too many differentially expressed miRNA with limma
limma
miRNA
Microarray
17 months ago
Sara
▴ 10
1
vote
4
replies
2.6k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 17 months ago by
Sarah
• 0
0
votes
17
replies
2.3k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 15 months ago by
Gordon Smyth
50k • written 18 months ago by
Sam
• 0
0
votes
1
reply
682
views
Compare different cell lines with tissues using limma
limma
MicroarrayData
Microarray
Agilent
updated 22 months ago by
Gordon Smyth
50k • written 22 months ago by
Sam
• 0
0
votes
8
replies
1.5k
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
22 months ago
YC
• 0
0
votes
4
replies
1.0k
views
Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray
DifferentialExpression
23 months ago
S
• 0
1
vote
2
replies
825
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
23 months ago
Mikołaj Mierzejewski
• 0
1
vote
2
replies
1.1k
views
Affymetrix analysis of microarray by using Limma
limma
MicroarrayData
Microarray
Affymetrix
23 months ago
Mikołaj Mierzejewski
• 0
4
votes
10
replies
1.9k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219
Microarray
oligo
AffymetrixChip
24 months ago
Yang Shi
▴ 10
3
votes
4
replies
1.7k
views
Quantile Normalization after rma or not?
limma
Microarray
oligo
24 months ago
Yang Shi
▴ 10
2
votes
2
replies
809
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db
Microarray
oligo
24 months ago
Yang Shi
▴ 10
2
votes
5
replies
1.8k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi
Microarray
2.0 years ago
nhaus
▴ 30
0
votes
2
replies
781
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db
MicroarrayData
Microarray
pd.clariom.d.human
2.0 years ago
amir.rakhimov.b
• 0
0
votes
2
replies
1.1k
views
Time course experiment using limma
limma
Multi-levelExperiments
Microarray
2.1 years ago
Wendy
• 0
0
votes
12
replies
1.5k
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
2.1 years ago
Adam
• 0
0
votes
0
replies
625
views
Error in svd(X) when using edge lrt (or odp) function.
edge
Microarray
longitudinal
2.2 years ago
emily
• 0
2
votes
5
replies
1.8k
views
Adjust for base line gene expression in limma model
limma
Microarray
updated 2.4 years ago by
Gordon Smyth
50k • written 2.4 years ago by
S
• 0
4
votes
6
replies
1.2k
views
RMA on different disease labels
rma
background
microarray
normalization
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Joshua
• 0
1
vote
1
reply
1.2k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
Caitlin
▴ 50
5
votes
2
replies
2.2k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray
limma
DifferentialExpression
updated 20 months ago by
Gordon Smyth
50k • written 2.7 years ago by
Nikshay
▴ 10
0
votes
1
reply
1.2k
views
Re-normalize microarray dataset in R
microarray
quantile
expression
R
Normalization
updated 2.8 years ago by
Konstantinos Yeles
▴ 80 • written 2.8 years ago by
mohammedtoufiq91
▴ 10
3
votes
5
replies
1.6k
views
Use of arrayWeights with two treatment groups
Microarray
arrays
limma
MicroarrayData
updated 2.9 years ago by
Gordon Smyth
50k • written 2.9 years ago by
Emma
• 0
1
vote
1
reply
1.3k
views
How do I adjust for other factors in Limma differential expression analysis?
limma
Microarray
MicroarrayData
arrays
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.0 years ago by
Emma
• 0
1
vote
2
replies
1.3k
views
RUV4 for microarrays
RUV4
RUV
Microarray
3.0 years ago
Antonio
• 0
0
votes
2
replies
2.1k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD
pcaMethods
MicroarrayData
Microarray
3.1 years ago
waiyin0923
• 0
0
votes
1
reply
879
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip
Microarray
affymetrix
updated 3.1 years ago by
Guido Hooiveld
★ 3.9k • written 3.1 years ago by
Pierre-Alex
• 0
1
vote
2
replies
1.3k
views
How to quantile normalize arraystar lncRNA microarray data?
limma
Microarray
3.1 years ago • updated 3.0 years ago
a.deb
• 0
3
votes
3
replies
1.3k
views
Weird MAplot with DEGs lying along the diagonals
limma
Microarray
AgilentChip
MA-plot
Normalization
3.2 years ago • updated 3.1 years ago
FedeXander
• 0
0
votes
2
replies
1.6k
views
WGCNA - Outliers after creating sample tree
MicroarrayData
WGCNA
Microarray
3.2 years ago
jpwl2
• 0
6
votes
4
replies
1.2k
views
Limma outputs different results for same sample?
topTable
MicroarrayData
ebayes
limma
Microarray
3.2 years ago
snijesh
▴ 20
1
vote
2
replies
1.4k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions
3factors
limma
Microarray
3.3 years ago • updated 3.2 years ago
Dan
▴ 20
3
votes
9
replies
1.5k
views
limma analysis when only Cy5 was used
MicroarrayData
limma
Microarray
3.3 years ago • updated 3.2 years ago
Daniel.Schnell
• 0
0
votes
0
replies
1.3k
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule
microarray
RNA-seq
WGCNA
3.6 years ago • updated 3.5 years ago
modarzi
▴ 10
1
vote
3
replies
2.4k
views
Annotating [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file
microarray
annotation
affy
3.6 years ago
kiera.lee
▴ 10
4
votes
7
replies
1.5k
views
Limma sample groups
microarray
limma
affy
cancer
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
nancy.nassar1590
• 0
0
votes
2
replies
1.2k
views
Regarding ArrayExpress package
microarray
arrayexpress
updated 3.6 years ago by
James W. MacDonald
65k • written 3.6 years ago by
akanksha17arora
• 0
0
votes
2
replies
1.1k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0
microarray
affy
r
3.6 years ago
Marco_aurelio
• 0
1
vote
6
replies
1.8k
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 9 months ago by
Gordon Smyth
50k • written 3.6 years ago by
linouhao
▴ 20
1
vote
6
replies
2.1k
views
TCGA: clinical data and expression data
microarray
annotation
cancer
updated 15 months ago by
Sharif
• 0 • written 3.7 years ago by
641549298
• 0
3
votes
1
reply
774
views
Create a '.db' package for agilent
R
agilent
microarray
updated 3.7 years ago by
James W. MacDonald
65k • written 3.7 years ago by
salamandra
▴ 20
0
votes
1
reply
828
views
Problem for installing arrayQualityMetrics package?
R
Microarray
updated 3.7 years ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
mathavanbioinfo
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: Log-cpm values from limma
by
Shaimaa Gamal
• 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Comment: DSS CpG coverage threshold
by
j.gilbert
• 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
Comment: deseq2 results
by
sajadahmad41454
• 0
could you please tell me if the results are fine or not? ![pca summary][1] ![pca plot][2] [1]: /media/images/ee7d8693-bcbe-4a7a-a566-d3…
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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