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Showing :
Microarray
•
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0
votes
1
reply
174
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray
Alignment
Biostrings
4 weeks ago • updated 29 days ago
sandmann.t
▴ 70
1
vote
2
replies
201
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
6 weeks ago
Abdul
▴ 20
2
votes
2
replies
266
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
7 weeks ago
Abdul
▴ 20
0
votes
2
replies
154
views
Full list of differential genes not obtained in topTable
Microarray
GEOquery
topTable
limma
updated 8 weeks ago by
Gordon Smyth
47k • written 8 weeks ago by
Ankita
• 0
1
vote
4
replies
804
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
2.7 years ago • updated 8 weeks ago
linouhao
▴ 20
2
votes
2
replies
194
views
Question about avereps function of limma
avereps
probes
average
limma
Microarray
updated 11 weeks ago by
Gordon Smyth
47k • written 11 weeks ago by
mohammedtoufiq91
▴ 10
0
votes
0
replies
183
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
3 months ago
jsharif
• 0
0
votes
1
reply
160
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 4 months ago by
James W. MacDonald
63k • written 4 months ago by
Aleksandra
• 0
0
votes
2
replies
281
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
4 months ago
dqt
• 0
0
votes
2
replies
260
views
Celfiles not reading in
Microarray
updated 4 months ago by
charlotteelouisean
• 0 • written 5 months ago by
Oluwaseun
• 0
1
vote
2
replies
4.6k
views
How to convert Illumina HT_12_v4 annotation
convert
R
annotation
microarray
illumina human ht-12 v4
updated 5 months ago by
snijesh
▴ 20 • written 5.5 years ago by
p_donchev84
• 0
1
vote
3
replies
361
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
updated 6 weeks ago by
Amanda
• 0 • written 6 months ago by
Sarah
• 0
6
votes
6
replies
798
views
Too many differentially expressed miRNA with limma
limma
miRNA
Microarray
6 months ago
Sara
▴ 10
0
votes
17
replies
1.1k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 3 months ago by
Gordon Smyth
47k • written 7 months ago by
Sam
• 0
0
votes
1
reply
363
views
Compare different cell lines with tissues using limma
limma
MicroarrayData
Microarray
Agilent
updated 11 months ago by
Gordon Smyth
47k • written 11 months ago by
Sam
• 0
0
votes
8
replies
824
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
11 months ago
YC
• 0
2
votes
13
replies
3.6k
views
Error in using r
microarray
updated 11 months ago by
17545106088
• 0 • written 6.6 years ago by
azhar
• 0
0
votes
4
replies
584
views
Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray
DifferentialExpression
11 months ago
S
• 0
1
vote
2
replies
454
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
12 months ago
Mikołaj Mierzejewski
• 0
1
vote
2
replies
517
views
Affymetrix analysis of microarray by using Limma
limma
MicroarrayData
Microarray
Affymetrix
12 months ago
Mikołaj Mierzejewski
• 0
4
votes
10
replies
1.1k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219
Microarray
oligo
AffymetrixChip
12 months ago
Yang Shi
▴ 10
3
votes
4
replies
767
views
Quantile Normalization after rma or not?
limma
Microarray
oligo
12 months ago
Yang Shi
▴ 10
2
votes
2
replies
435
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db
Microarray
oligo
12 months ago
Yang Shi
▴ 10
2
votes
5
replies
807
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi
Microarray
12 months ago
nhaus
• 0
0
votes
2
replies
408
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db
MicroarrayData
Microarray
pd.clariom.d.human
13 months ago
amir.rakhimov.b
• 0
0
votes
2
replies
593
views
Time course experiment using limma
limma
Multi-levelExperiments
Microarray
13 months ago
Wendy
• 0
0
votes
12
replies
913
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
13 months ago
Adam
• 0
0
votes
0
replies
343
views
Error in svd(X) when using edge lrt (or odp) function.
edge
Microarray
longitudinal
14 months ago
emily
• 0
1
vote
7
replies
5.7k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray
normalization
oligo HTA
updated 14 months ago by
Harald
• 0 • written 4.4 years ago by
RV
▴ 10
2
votes
5
replies
1.2k
views
Adjust for base line gene expression in limma model
limma
Microarray
updated 17 months ago by
Gordon Smyth
47k • written 17 months ago by
S
• 0
4
votes
6
replies
747
views
RMA on different disease labels
rma
background
microarray
normalization
updated 19 months ago by
James W. MacDonald
63k • written 19 months ago by
Joshua
• 0
1
vote
1
reply
724
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 20 months ago by
James W. MacDonald
63k • written 20 months ago by
Caitlin
▴ 50
5
votes
2
replies
1.2k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray
limma
DifferentialExpression
updated 9 months ago by
Gordon Smyth
47k • written 21 months ago by
Nikshay
▴ 10
0
votes
1
reply
773
views
Re-normalize microarray dataset in R
microarray
quantile
expression
R
Normalization
updated 22 months ago by
Konstantinos Yeles
▴ 80 • written 22 months ago by
mohammedtoufiq91
▴ 10
3
votes
5
replies
965
views
Use of arrayWeights with two treatment groups
Microarray
arrays
limma
MicroarrayData
updated 23 months ago by
Gordon Smyth
47k • written 24 months ago by
Emma
• 0
1
vote
1
reply
684
views
How do I adjust for other factors in Limma differential expression analysis?
limma
Microarray
MicroarrayData
arrays
updated 2.0 years ago by
Kevin Blighe
3.8k • written 2.1 years ago by
Emma
• 0
1
vote
2
replies
845
views
RUV4 for microarrays
RUV4
RUV
Microarray
2.1 years ago
Antonio
• 0
0
votes
2
replies
1.5k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD
pcaMethods
MicroarrayData
Microarray
2.1 years ago
waiyin0923
• 0
0
votes
1
reply
572
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip
Microarray
affymetrix
updated 2.1 years ago by
Guido Hooiveld
★ 3.6k • written 2.1 years ago by
Pierre-Alex
• 0
1
vote
2
replies
802
views
How to quantile normalize arraystar lncRNA microarray data?
limma
Microarray
2.2 years ago • updated 2.1 years ago
a.deb
• 0
3
votes
3
replies
866
views
Weird MAplot with DEGs lying along the diagonals
limma
Microarray
AgilentChip
MA-plot
Normalization
2.2 years ago
FedeXander
• 0
0
votes
2
replies
1.1k
views
WGCNA - Outliers after creating sample tree
MicroarrayData
WGCNA
Microarray
2.3 years ago
jpwl2
• 0
6
votes
4
replies
877
views
Limma outputs different results for same sample?
topTable
MicroarrayData
ebayes
limma
Microarray
2.3 years ago
snijesh
▴ 20
1
vote
2
replies
1.0k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions
3factors
limma
Microarray
2.3 years ago
Dan
▴ 20
3
votes
9
replies
1.0k
views
limma analysis when only Cy5 was used
MicroarrayData
limma
Microarray
2.3 years ago
Daniel.Schnell
• 0
0
votes
1
reply
954
views
Creating a model matrix for three age groups using two-colour arrays
Microarray
BRAIN
Microarray
BRAIN
updated 2.3 years ago by
Gordon Smyth
47k • written 14.5 years ago by
Carthika Luxmanan
▴ 10
5
votes
8
replies
2.0k
views
how to annotate arrays
affy
annotation
microarray
oligo
updated 2.5 years ago by
James W. MacDonald
63k • written 7.8 years ago by
ben_cossins
• 0
0
votes
1
reply
743
views
Normalisation of protein micro array data using VSN
microarray
normalization
protein
updated 2.6 years ago by
Wolfgang Huber
13k • written 4.0 years ago by
keniajin
• 0
0
votes
2
replies
627
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi
minfi
microarray
epic
3.1 years ago • updated 2.6 years ago
Nala
• 0
0
votes
0
replies
975
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule
microarray
RNA-seq
WGCNA
2.6 years ago
modarzi
▴ 10
50 results • Page
1 of 1
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Replies
Comment: Question on constructing design matrix and defining contrasts for analysis
by
mohammedtoufiq91
▴ 10
@gordonsmyth thank you, yes, please find the targets frame below. Basically, I want to create a design matrix and binarize by 0 and 1 to be…
Comment: WGCNA: many over and under-expressed features in modules of a signed network
by
andres.firrincieli
▴ 50
answered in Biostars: https://www.biostars.org/p/9564943/
Comment: Multitasking and Rbwa
by
Jean-Philippe Fortin
• 0
Indeed, one can pass additional arguments to the `bwa_aln` function in `Rbwa`: bwa_aln(type="single", index_prefix=index_pr…
Comment: biomaRt error: database disk image is malformed
by
Emile
• 0
UNBORKING the bioMaRt cache `biomaRt::biomartCacheClear()` also fixes the troubles with PANTHER.db installation which have also something t…
Answer: Proteomics data with NA values
by
Laurent Gatto
1.6k
- First, you need to assess how many missing values you have. - I would recommend not to impute your data by 0 (or any arbitrary small …
Votes
Answer: Question on constructing design matrix and defining contrasts for analysis
WGCNA: many over and under-expressed features in modules of a signed network
Comment: WGCNA: many over and under-expressed features in modules of a signed network
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Answer: Normalized counts from LRT or Wald test?
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