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MicroarrayData
•
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0
votes
0
replies
307
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
6 months ago
Shaimaa Gamal
• 0
0
votes
1
reply
298
views
Ph.D. scholar
WGCNA
DataNormalization
MicroarrayData
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
Harshul
• 0
1
vote
2
replies
1.4k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
11 months ago
Ai
• 0
1
vote
2
replies
727
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
19 months ago
Mj.A.
▴ 20
5
votes
7
replies
1.5k
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
Amit
• 0
2
votes
6
replies
1.5k
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
19 months ago
Lily Cheang
▴ 10
0
votes
3
replies
1.1k
views
Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData
hta20transcriptcluster.db
updated 2.2 years ago by
Gordon Smyth
53k • written 2.2 years ago by
yaxade2481
• 0
5
votes
8
replies
2.9k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 22 months ago by
Shaimaa Gamal
• 0 • written 2.4 years ago by
pg45863
▴ 10
1
vote
2
replies
1.3k
views
Error in getCdfInfo(object) :
MicroarrayData
2.5 years ago
kobra
• 0
0
votes
0
replies
1.0k
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
2.7 years ago
agamemnon
• 0
2
votes
1
reply
986
views
Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData
Annotation
GEOdata
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Michele Claire
• 0
0
votes
1
reply
1.1k
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Aleksandra
• 0
0
votes
2
replies
1.7k
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
2.8 years ago
dqt
• 0
2
votes
2
replies
1.0k
views
2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip
MicroarrayData
Anova
3.0 years ago
evan.j.williams
▴ 10
0
votes
17
replies
4.1k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 2.7 years ago by
Gordon Smyth
53k • written 3.0 years ago by
Sam
• 0
0
votes
1
reply
826
views
Finding negative control in the array using R
R
MicroarrayData
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Fatemeh
• 0
0
votes
0
replies
803
views
Filtering single-channel Affymetrix probes
filtering
probe
MicroarrayData
3.2 years ago
Fatemeh
• 0
2
votes
2
replies
1.8k
views
the difference between getGEO and getGEOSuppFiles
MicroarrayData
3.2 years ago
Fatemeh
• 0
1
vote
1
reply
909
views
IS DGE possible with normalized microarray expression data and Limma ?
limma
MicroarrayData
updated 3.2 years ago by
James W. MacDonald
68k • written 3.2 years ago by
waltheja
• 0
0
votes
1
reply
1.1k
views
Compare different cell lines with tissues using limma
limma
MicroarrayData
Microarray
Agilent
updated 3.3 years ago by
Gordon Smyth
53k • written 3.3 years ago by
Sam
• 0
0
votes
8
replies
2.2k
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
3.3 years ago
YC
• 0
1
vote
2
replies
1.3k
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
3.4 years ago
Mikołaj Mierzejewski
• 0
1
vote
2
replies
1.8k
views
Affymetrix analysis of microarray by using Limma
limma
MicroarrayData
Microarray
Affymetrix
3.4 years ago
Mikołaj Mierzejewski
• 0
0
votes
2
replies
1.2k
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db
MicroarrayData
Microarray
pd.clariom.d.human
3.5 years ago
amir.rakhimov.b
• 0
0
votes
2
replies
1.2k
views
How to extract probe level intensity after rma() normalization
MicroarrayData
AffymetrixChip
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
Haoran
• 0
0
votes
4
replies
1.4k
views
getProbeInfo and exprs return two different dimensions
CELfile
MicroarrayData
AffymetrixChip
3.6 years ago
Haoran
• 0
0
votes
1
reply
1.3k
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar
DEGseq
MicroarrayData
updated 3.9 years ago by
James W. MacDonald
68k • written 3.9 years ago by
biomyscience
• 0
0
votes
1
reply
1.1k
views
Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr
raw
Agilent
MicroarrayData
import
updated 4.0 years ago by
Gordon Smyth
53k • written 4.0 years ago by
irina.st.louis4
• 0
1
vote
3
replies
1.7k
views
Microarray - Illumina Metadata
limma
GEO
MicroarrayData
affy
updated 4.1 years ago by
James W. MacDonald
68k • written 4.1 years ago by
RMP87
• 0
0
votes
2
replies
884
views
Adj. P-value identical and high for all the genes
MicroarrayData
4.1 years ago
Adriana
• 0
1
vote
1
reply
1.7k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 4.1 years ago by
James W. MacDonald
68k • written 4.1 years ago by
Caitlin
▴ 50
3
votes
5
replies
2.4k
views
Use of arrayWeights with two treatment groups
Microarray
arrays
limma
MicroarrayData
updated 4.3 years ago by
Gordon Smyth
53k • written 4.4 years ago by
Emma
• 0
1
vote
1
reply
2.1k
views
How do I adjust for other factors in Limma differential expression analysis?
limma
Microarray
MicroarrayData
arrays
updated 4.4 years ago by
Kevin Blighe
★ 4.0k • written 4.4 years ago by
Emma
• 0
0
votes
2
replies
2.6k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD
pcaMethods
MicroarrayData
Microarray
4.5 years ago
waiyin0923
• 0
0
votes
2
replies
2.3k
views
WGCNA - Outliers after creating sample tree
MicroarrayData
WGCNA
Microarray
4.7 years ago
jpwl2
• 0
9
votes
4
replies
1.9k
views
Limma outputs different results for same sample?
topTable
MicroarrayData
ebayes
limma
Microarray
4.7 years ago
snijesh
▴ 200
3
votes
9
replies
2.2k
views
limma analysis when only Cy5 was used
MicroarrayData
limma
Microarray
4.7 years ago
Daniel.Schnell
• 0
37 results • Page
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
by
teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Votes
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
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