Showing : Microarray • reset
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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
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2
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201
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
6 weeks ago Abdul ▴ 20
2
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2
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266
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
7 weeks ago Abdul ▴ 20
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2
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154
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Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 8 weeks ago by 47k • written 8 weeks ago by • 0
1
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4
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804
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can negative value microarray matrix data analysed by limma directly
limma microarray normalization
2.7 years ago • updated 8 weeks ago linouhao ▴ 20
2
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2
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194
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Question about avereps function of limma
avereps probes average limma Microarray
updated 11 weeks ago by 47k • written 11 weeks ago by ▴ 10
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183
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
3 months ago jsharif • 0
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1
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160
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 4 months ago by 63k • written 4 months ago by • 0
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2
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281
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
4 months ago dqt • 0
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2
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260
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Celfiles not reading in
Microarray
updated 4 months ago by • 0 • written 5 months ago by • 0
1
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2
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4.6k
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How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 5 months ago by ▴ 20 • written 5.5 years ago by • 0
1
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3
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361
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
updated 6 weeks ago by • 0 • written 6 months ago by • 0
6
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6
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798
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Too many differentially expressed miRNA with limma
limma miRNA Microarray
6 months ago Sara ▴ 10
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17
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1.1k
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Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 3 months ago by 47k • written 7 months ago by • 0
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1
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363
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Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 11 months ago by 47k • written 11 months ago by • 0
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8
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824
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
11 months ago YC • 0
2
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13
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3.6k
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Error in using r
microarray
updated 11 months ago by • 0 • written 6.6 years ago by • 0
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4
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584
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Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
11 months ago S • 0
1
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2
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454
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
12 months ago Mikołaj Mierzejewski • 0
1
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2
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517
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
12 months ago Mikołaj Mierzejewski • 0
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10
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1.1k
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Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
12 months ago Yang Shi ▴ 10
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4
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767
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Quantile Normalization after rma or not?
limma Microarray oligo
12 months ago Yang Shi ▴ 10
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2
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435
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Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
12 months ago Yang Shi ▴ 10
2
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5
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807
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Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
12 months ago nhaus • 0
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2
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408
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
13 months ago amir.rakhimov.b • 0
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2
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593
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Time course experiment using limma
limma Multi-levelExperiments Microarray
13 months ago Wendy • 0
0
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12
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913
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Annotating featureData to an affymetrix Xcel microarray
Microarray
13 months ago Adam • 0
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0
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343
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Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
14 months ago emily • 0
1
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7
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5.7k
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Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 14 months ago by • 0 • written 4.4 years ago by ▴ 10
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5
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1.2k
views
Adjust for base line gene expression in limma model
limma Microarray
updated 17 months ago by 47k • written 17 months ago by • 0
4
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6
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747
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RMA on different disease labels
rma background microarray normalization
updated 19 months ago by 63k • written 19 months ago by • 0
1
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1
reply
724
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Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 20 months ago by 63k • written 20 months ago by ▴ 50
5
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2
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1.2k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 9 months ago by 47k • written 21 months ago by ▴ 10
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1
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773
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Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 22 months ago by ▴ 80 • written 22 months ago by ▴ 10
3
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5
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965
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Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 23 months ago by 47k • written 24 months ago by • 0
1
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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 3.8k • written 2.1 years ago by • 0
1
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2
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845
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RUV4 for microarrays
RUV4 RUV Microarray
2.1 years ago Antonio • 0
0
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2
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1.5k
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
2.1 years ago waiyin0923 • 0
0
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1
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572
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Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 2.1 years ago by ★ 3.6k • written 2.1 years ago by • 0
1
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2
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802
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How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
2.2 years ago • updated 2.1 years ago a.deb • 0
3
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3
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866
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Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
2.2 years ago FedeXander • 0
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2
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1.1k
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WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
2.3 years ago jpwl2 • 0
6
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4
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877
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Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
2.3 years ago snijesh ▴ 20
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2
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1.0k
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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
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9
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1.0k
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limma analysis when only Cy5 was used
MicroarrayData limma Microarray
2.3 years ago Daniel.Schnell • 0
0
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1
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954
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Creating a model matrix for three age groups using two-colour arrays
Microarray BRAIN Microarray BRAIN
updated 2.3 years ago by 47k • written 14.5 years ago by ▴ 10
5
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8
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2.0k
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how to annotate arrays
affy annotation microarray oligo
updated 2.5 years ago by 63k • written 7.8 years ago by • 0
0
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1
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743
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Normalisation of protein micro array data using VSN
microarray normalization protein
updated 2.6 years ago by 13k • written 4.0 years ago by • 0
0
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2
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627
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Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
3.1 years ago • updated 2.6 years ago Nala • 0
0
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0
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975
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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
Recent ...
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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