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hugene20
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DE analysis pipeline with Hugene 2.0 ST arrays
hugene20
microarray
limma
limma paired analysis
oligo
7.0 years ago
hakimelakhrass
• 0
2
votes
2
replies
2.4k
views
HuGene 2.0 ST CDF files and xps
xps
hugene20
updated 8.3 years ago by
cstrato
★ 3.9k • written 8.3 years ago by
Alison Ziesel
▴ 60
0
votes
3
replies
2.2k
views
Reading Affymetrix data from pd.hugene.2.0.st using affy
affy
pd.hugene.2.0.st
hugene20
annotation
microarray
7.9 years ago
kanacska
▴ 10
0
votes
3
replies
2.1k
views
HUgene 2.0 analyses with CEL files, oligo package
microarray
annotation
hgu133plus2
hugene20
7.9 years ago • updated 7.8 years ago
kanacska
▴ 10
0
votes
4
replies
1.9k
views
HUgene 2.0 analyses heatmap
hugene20
heatmap
affymetrixchip
updated 7.7 years ago by
alakatos
▴ 120 • written 7.7 years ago by
kanacska
▴ 10
4
votes
10
replies
1.8k
views
Limma/oligo always crashing
limma
microarray
pd.hugene.2.0.st
hugene20
oligo
7.0 years ago
hakimelakhrass
• 0
3
votes
10
replies
1.4k
views
Still need help identifying a good workflow for finding DEG in hugene 2.0 st
microarray
hugene20
limma
oligo
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
hakimelakhrass
• 0
7 results • Page
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Comment: MA plot
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