Showing : Microarray • reset
4
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10
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176
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Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
3 days ago • updated 2 days ago Yang Shi • 0
3
votes
4
replies
112
views
Quantile Normalization after rma or not?
limma Microarray oligo
4 days ago • updated 3 days ago Yang Shi • 0
2
votes
2
replies
75
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
6 days ago Yang Shi • 0
2
votes
5
replies
147
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Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
13 days ago • updated 12 days ago nhaus • 0
0
votes
2
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101
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
19 days ago • updated 17 days ago amir.rakhimov.b • 0
0
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2
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148
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Time course experiment using limma
limma Multi-levelExperiments Microarray
5 weeks ago • updated 4 weeks ago Wendy • 0
0
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12
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352
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Annotating featureData to an affymetrix Xcel microarray
Microarray
6 weeks ago • updated 5 weeks ago Adam • 0
0
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0
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109
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Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
10 weeks ago emily • 0
1
vote
7
replies
3.6k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 9 weeks ago by • 0 • written 3.3 years ago by ▴ 10
2
votes
5
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514
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Adjust for base line gene expression in limma model
limma Microarray
updated 4 months ago by 45k • written 5 months ago by • 0
4
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6
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392
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RMA on different disease labels
rma background microarray normalization
updated 6 months ago by 59k • written 6 months ago by • 0
1
vote
1
reply
440
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 8 months ago by 59k • written 8 months ago by ▴ 50
4
votes
2
replies
394
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
9 months ago Nikshay ▴ 10
0
votes
1
reply
336
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 10 months ago by ▴ 70 • written 10 months ago by ▴ 10
3
votes
5
replies
500
views
Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 10 months ago by 45k • written 11 months ago by • 0
1
vote
1
reply
336
views
How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 12 months ago by 3.5k • written 12 months ago by • 0
1
vote
2
replies
434
views
RUV4 for microarrays
RUV4 RUV Microarray
12 months ago Antonio • 0
0
votes
2
replies
690
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
13 months ago waiyin0923 • 0
0
votes
1
reply
297
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 13 months ago by ★ 3.2k • written 13 months ago by • 0
1
vote
2
replies
366
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How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
13 months ago a.deb • 0
3
votes
3
replies
546
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
14 months ago Federico Alessandro • 0
0
votes
2
replies
510
views
WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
15 months ago jpwl2 • 0
5
votes
4
replies
491
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
15 months ago snijesh ▴ 20
1
vote
2
replies
609
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
15 months ago Dan ▴ 10
3
votes
9
replies
597
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
15 months ago Daniel.Schnell • 0
0
votes
1
reply
692
views
Creating a model matrix for three age groups using two-colour arrays
Microarray BRAIN Microarray BRAIN
updated 16 months ago by 45k • written 13.5 years ago by ▴ 10
5
votes
8
replies
1.6k
views
how to annotate arrays
affy annotation microarray oligo
updated 17 months ago by 59k • written 6.8 years ago by • 0
0
votes
1
reply
460
views
Normalisation of protein micro array data using VSN
microarray normalization protein
updated 18 months ago by 13k • written 2.9 years ago by • 0
0
votes
2
replies
351
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
2.1 years ago • updated 19 months ago Nala • 0
0
votes
0
replies
637
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
19 months ago modarzi ▴ 10
1
vote
3
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1.0k
views
Annotating [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file
microarray annotation affy
19 months ago kiera.lee ▴ 10
4
votes
7
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633
views
Limma sample groups
microarray limma affy cancer
updated 20 months ago by 45k • written 20 months ago by • 0
0
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2
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503
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Regarding ArrayExpress package
microarray arrayexpress
updated 20 months ago by 59k • written 20 months ago by • 0
0
votes
2
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456
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What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0 microarray affy r
20 months ago Marco_aurelio • 0
0
votes
2
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327
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 20 months ago by 3.5k • written 20 months ago by ▴ 20
1
vote
5
replies
636
views
TCGA: clinical data and expression data
microarray annotation cancer
updated 20 months ago by 3.5k • written 20 months ago by • 0
3
votes
1
reply
320
views
Create a '.db' package for agilent
R agilent microarray
updated 20 months ago by 59k • written 20 months ago by ▴ 20
0
votes
1
reply
360
views
Problem for installing arrayQualityMetrics package?
R Microarray
updated 21 months ago by 3.5k • written 21 months ago by ▴ 20
0
votes
1
reply
237
views
Input of tscR
microarray normalization tscR time-course
updated 22 months ago by 3.5k • written 22 months ago by • 0
1
vote
1
reply
418
views
Error in GO enrichment with topGO
topGO microarray Gene ontology
updated 22 months ago by 59k • written 22 months ago by ▴ 10
1
vote
2
replies
333
views
How to construct matrix and fit linear model for this microarray?
microarray dge matrix makecontrasts limma
updated 22 months ago by 45k • written 22 months ago by ▴ 10
2
votes
3
replies
427
views
Annotation package generation for HTA-2_0 by pdInfoBuilder fails
microarray pdInfoBuilder oligo
updated 22 months ago by 59k • written 22 months ago by • 0
5
votes
9
replies
768
views
Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray affy
updated 23 months ago by 3.5k • written 23 months ago by ▴ 10
0
votes
2
replies
9.3k
views
Installing EnhancedVolcano package in R
microarray software error
updated 23 months ago by 3.5k • written 23 months ago by • 0
1
vote
1
reply
259
views
Problem in analyzing microarray with duplicate or triplicate data
microarray limma
23 months ago peirinl • 0
1
vote
4
replies
353
views
How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 23 months ago by 59k • written 23 months ago by ▴ 10
0
votes
2
replies
361
views
How to process triplicate cel data?
microarray affy cel drugmatrix
updated 23 months ago by 45k • written 23 months ago by • 0
6
votes
3
replies
533
views
GEOquery: preprocessing log of imported data
GEOquery microarray lumi affy limma
updated 23 months ago by 21k • written 23 months ago by ▴ 40
1
vote
2
replies
744
views
Partial NA coefficients for 10 probe(s) Limma
limma microarray cancer
updated 2.1 years ago by 3.5k • written 2.1 years ago by • 0
0
votes
4
replies
479
views
Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 2.1 years ago by 45k • written 2.2 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Ok.. thanks for your valuable suggestion and quick replies. I have generated an MA plot using plotMASwish. thanks ekta
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by Michael Love 37k
Sorry, I haven't seen this. Maybe try filtering low count genes? ``` keep <- rowSums(counts(dds) >= 10) >= X dds <- dds[keep,] # then run …
Comment: Transcript-level differential expression using DESeq2 by Michael Love 37k
To show some extent of the DTE you can plot the LFC of the significant set and their mean count, we have `plotMASwish` to do this. Another…
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
No, the Volcano plot is not essential. I just wanted to show DETs with the help of a plot. Could you suggest a way for it? What are the oth…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Votes
Comment: Transcript-level differential expression using DESeq2
Comment: Transcript-level differential expression using DESeq2
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
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