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Showing :
Microarray
•
reset
4
votes
10
replies
176
views
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
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi
Microarray
13 days ago • updated 12 days ago
nhaus
• 0
0
votes
2
replies
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
votes
2
replies
148
views
Time course experiment using limma
limma
Multi-levelExperiments
Microarray
5 weeks ago • updated 4 weeks ago
Wendy
• 0
0
votes
12
replies
352
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
6 weeks ago • updated 5 weeks ago
Adam
• 0
0
votes
0
replies
109
views
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
Harald
• 0 • written 3.3 years ago by
RV
▴ 10
2
votes
5
replies
514
views
Adjust for base line gene expression in limma model
limma
Microarray
updated 4 months ago by
Gordon Smyth
45k • written 5 months ago by
S
• 0
4
votes
6
replies
392
views
RMA on different disease labels
rma
background
microarray
normalization
updated 6 months ago by
James W. MacDonald
59k • written 6 months ago by
Joshua
• 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
James W. MacDonald
59k • written 8 months ago by
Caitlin
▴ 50
4
votes
2
replies
394
views
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
Konstantinos Yeles
▴ 70 • written 10 months ago by
mohammedtoufiq91
▴ 10
3
votes
5
replies
500
views
Use of arrayWeights with two treatment groups
Microarray
arrays
limma
MicroarrayData
updated 10 months ago by
Gordon Smyth
45k • written 11 months ago by
Emma
• 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
Kevin Blighe
3.5k • written 12 months ago by
Emma
• 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
Guido Hooiveld
★ 3.2k • written 13 months ago by
Pierre-Alex
• 0
1
vote
2
replies
366
views
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
Gordon Smyth
45k • written 13.5 years ago by
Carthika Luxmanan
▴ 10
5
votes
8
replies
1.6k
views
how to annotate arrays
affy
annotation
microarray
oligo
updated 17 months ago by
James W. MacDonald
59k • written 6.8 years ago by
ben_cossins
• 0
0
votes
1
reply
460
views
Normalisation of protein micro array data using VSN
microarray
normalization
protein
updated 18 months ago by
Wolfgang Huber
13k • written 2.9 years ago by
keniajin
• 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
replies
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
replies
633
views
Limma sample groups
microarray
limma
affy
cancer
updated 20 months ago by
Gordon Smyth
45k • written 20 months ago by
nancy.nassar1590
• 0
0
votes
2
replies
503
views
Regarding ArrayExpress package
microarray
arrayexpress
updated 20 months ago by
James W. MacDonald
59k • written 20 months ago by
akanksha17arora
• 0
0
votes
2
replies
456
views
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
replies
327
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 20 months ago by
Kevin Blighe
3.5k • written 20 months ago by
linouhao
▴ 20
1
vote
5
replies
636
views
TCGA: clinical data and expression data
microarray
annotation
cancer
updated 20 months ago by
Kevin Blighe
3.5k • written 20 months ago by
641549298
• 0
3
votes
1
reply
320
views
Create a '.db' package for agilent
R
agilent
microarray
updated 20 months ago by
James W. MacDonald
59k • written 20 months ago by
salamandra
▴ 20
0
votes
1
reply
360
views
Problem for installing arrayQualityMetrics package?
R
Microarray
updated 21 months ago by
Kevin Blighe
3.5k • written 21 months ago by
mathavanbioinfo
▴ 20
0
votes
1
reply
237
views
Input of tscR
microarray
normalization
tscR
time-course
updated 22 months ago by
Kevin Blighe
3.5k • written 22 months ago by
keremwai
• 0
1
vote
1
reply
418
views
Error in GO enrichment with topGO
topGO
microarray
Gene ontology
updated 22 months ago by
James W. MacDonald
59k • written 22 months ago by
June.
▴ 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
Gordon Smyth
45k • written 22 months ago by
June.
▴ 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
James W. MacDonald
59k • written 22 months ago by
Marton Papp
• 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
Kevin Blighe
3.5k • written 23 months ago by
adR
▴ 10
0
votes
2
replies
9.3k
views
Installing EnhancedVolcano package in R
microarray
software error
updated 23 months ago by
Kevin Blighe
3.5k • written 23 months ago by
kanwal.zahid.siddiqi
• 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
James W. MacDonald
59k • written 23 months ago by
Sam
▴ 10
0
votes
2
replies
361
views
How to process triplicate cel data?
microarray
affy
cel
drugmatrix
updated 23 months ago by
Gordon Smyth
45k • written 23 months ago by
peirinl
• 0
6
votes
3
replies
533
views
GEOquery: preprocessing log of imported data
GEOquery
microarray
lumi
affy
limma
updated 23 months ago by
Sean Davis
21k • written 23 months ago by
fabian
▴ 40
1
vote
2
replies
744
views
Partial NA coefficients for 10 probe(s) Limma
limma
microarray
cancer
updated 2.1 years ago by
Kevin Blighe
3.5k • written 2.1 years ago by
everardoremi
• 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
Gordon Smyth
45k • written 2.2 years ago by
Natalia
• 0
50 results • Page
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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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