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MicroarrayData
•
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0
votes
0
replies
427
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
9 months ago
Shaimaa Gamal
• 0
0
votes
1
reply
376
views
Ph.D. scholar
WGCNA
DataNormalization
MicroarrayData
updated 11 months ago by
ATpoint
★ 5.0k • written 12 months ago by
Harshul
• 0
1
vote
2
replies
1.5k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
14 months ago
Ai
• 0
1
vote
2
replies
807
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
22 months ago
Mj.A.
▴ 20
5
votes
7
replies
1.7k
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 22 months ago by
Gordon Smyth
53k • written 22 months ago by
Amit
• 0
2
votes
6
replies
1.7k
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
22 months ago
Lily Cheang
▴ 10
0
votes
3
replies
1.2k
views
Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData
hta20transcriptcluster.db
updated 2.4 years ago by
Gordon Smyth
53k • written 2.4 years ago by
yaxade2481
• 0
5
votes
8
replies
3.2k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 2.1 years ago by
Shaimaa Gamal
• 0 • written 2.7 years ago by
pg45863
▴ 10
1
vote
2
replies
1.5k
views
Error in getCdfInfo(object) :
MicroarrayData
2.8 years ago
kobra
• 0
0
votes
0
replies
1.2k
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
2.9 years ago
agamemnon
• 0
2
votes
1
reply
1.1k
views
Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData
Annotation
GEOdata
updated 2.9 years ago by
James W. MacDonald
68k • written 2.9 years ago by
Michele Claire
• 0
0
votes
1
reply
1.2k
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
Aleksandra
• 0
0
votes
2
replies
1.8k
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
3.0 years ago
dqt
• 0
2
votes
2
replies
1.1k
views
2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip
MicroarrayData
Anova
3.2 years ago
evan.j.williams
▴ 10
0
votes
17
replies
4.5k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 3.0 years ago by
Gordon Smyth
53k • written 3.2 years ago by
Sam
• 0
0
votes
1
reply
896
views
Finding negative control in the array using R
R
MicroarrayData
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
Fatemeh
• 0
0
votes
0
replies
848
views
Filtering single-channel Affymetrix probes
filtering
probe
MicroarrayData
3.4 years ago
Fatemeh
• 0
2
votes
2
replies
2.1k
views
the difference between getGEO and getGEOSuppFiles
MicroarrayData
3.4 years ago
Fatemeh
• 0
1
vote
1
reply
962
views
IS DGE possible with normalized microarray expression data and Limma ?
limma
MicroarrayData
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
waltheja
• 0
0
votes
1
reply
1.3k
views
Compare different cell lines with tissues using limma
limma
MicroarrayData
Microarray
Agilent
updated 3.6 years ago by
Gordon Smyth
53k • written 3.6 years ago by
Sam
• 0
0
votes
8
replies
2.3k
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
3.6 years ago
YC
• 0
1
vote
2
replies
1.4k
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
3.6 years ago
Mikołaj Mierzejewski
• 0
1
vote
2
replies
1.9k
views
Affymetrix analysis of microarray by using Limma
limma
MicroarrayData
Microarray
Affymetrix
3.6 years ago
Mikołaj Mierzejewski
• 0
0
votes
2
replies
1.3k
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db
MicroarrayData
Microarray
pd.clariom.d.human
3.7 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 3.7 years ago by
James W. MacDonald
68k • written 3.7 years ago by
Haoran
• 0
0
votes
4
replies
1.4k
views
getProbeInfo and exprs return two different dimensions
CELfile
MicroarrayData
AffymetrixChip
3.8 years ago
Haoran
• 0
0
votes
1
reply
1.4k
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar
DEGseq
MicroarrayData
updated 4.1 years ago by
James W. MacDonald
68k • written 4.1 years ago by
biomyscience
• 0
0
votes
1
reply
1.2k
views
Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr
raw
Agilent
MicroarrayData
import
updated 4.2 years ago by
Gordon Smyth
53k • written 4.2 years ago by
irina.st.louis4
• 0
1
vote
3
replies
1.8k
views
Microarray - Illumina Metadata
limma
GEO
MicroarrayData
affy
updated 4.3 years ago by
James W. MacDonald
68k • written 4.3 years ago by
RMP87
• 0
0
votes
2
replies
964
views
Adj. P-value identical and high for all the genes
MicroarrayData
4.3 years ago
Adriana
• 0
1
vote
1
reply
1.8k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 4.4 years ago by
James W. MacDonald
68k • written 4.4 years ago by
Caitlin
▴ 50
3
votes
5
replies
2.6k
views
Use of arrayWeights with two treatment groups
Microarray
arrays
limma
MicroarrayData
updated 4.6 years ago by
Gordon Smyth
53k • written 4.6 years ago by
Emma
• 0
1
vote
1
reply
2.2k
views
How do I adjust for other factors in Limma differential expression analysis?
limma
Microarray
MicroarrayData
arrays
updated 4.7 years ago by
Kevin Blighe
★ 4.0k • written 4.7 years ago by
Emma
• 0
0
votes
2
replies
2.9k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD
pcaMethods
MicroarrayData
Microarray
4.8 years ago
waiyin0923
• 0
0
votes
2
replies
2.4k
views
WGCNA - Outliers after creating sample tree
MicroarrayData
WGCNA
Microarray
4.9 years ago
jpwl2
• 0
9
votes
4
replies
2.0k
views
Limma outputs different results for same sample?
topTable
MicroarrayData
ebayes
limma
Microarray
4.9 years ago
snijesh
▴ 200
3
votes
9
replies
2.3k
views
limma analysis when only Cy5 was used
MicroarrayData
limma
Microarray
5.0 years ago • updated 4.9 years ago
Daniel.Schnell
• 0
37 results • Page
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Comment: Pairwise comparison of multiple groups with different base
by
ja569116
• 0
Hi @mikelove I have a similar situation, and I feel that I have interpreted the results in the wrong way. In my case I would like to identi…
Comment: Are individual-mouse-based statistics possible in CellChat?
by
TikTsossakaas33ocissalpc
• 0
Questions about comparing groups and statistical significance highlight how data driven thinking matters across fields. In online mobile ga…
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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