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DE analysis pipeline with Hugene 2.0 ST arrays
hugene20 microarray limma limma paired analysis oligo
6.0 years ago hakimelakhrass • 0
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HuGene 2.0 ST CDF files and xps
xps hugene20
updated 7.3 years ago by ★ 3.9k • written 7.3 years ago by ▴ 60
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Reading Affymetrix data from pd.hugene.2.0.st using affy
affy pd.hugene.2.0.st hugene20 annotation microarray
6.8 years ago kanacska ▴ 10
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1.9k
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HUgene 2.0 analyses with CEL files, oligo package
microarray annotation hgu133plus2 hugene20
6.8 years ago kanacska ▴ 10
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4
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HUgene 2.0 analyses heatmap
hugene20 heatmap affymetrixchip
updated 6.7 years ago by ▴ 110 • written 6.7 years ago by ▴ 10
4
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10
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Limma/oligo always crashing
limma microarray pd.hugene.2.0.st hugene20 oligo
6.0 years ago hakimelakhrass • 0
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Still need help identifying a good workflow for finding DEG in hugene 2.0 st
microarray hugene20 limma oligo
updated 6.0 years ago by ★ 27k • written 6.0 years ago by • 0
7 results • Page 1 of 1
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Comment: Uniform window size for different genes by rbenel ▴ 20
Thanks, I'll keep working on it because the `png("two_transcripts.ong", 240)` still looks a bit weird... thanks though!
Comment: DTU using DEXSeq (time series data with condition factor) by Alejandro Reyes ★ 1.8k
Apologies for late reply, Nirad. You probably figured it out by now. In the formulae, the 'exon' term would take the baseline transcript us…
Comment: DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ens by Alejandro Reyes ★ 1.8k
Apologies for late reply. Could you share the link to the gtf source?
Answer: Normalizing exonic reads and then log transforming or variance stabilising by Alejandro Reyes ★ 1.8k
Hello. Short answer is yes, count-level transoformation for variance stabilization also work for exon-count level matrices.
Comment: A mistake came when I install some packages using "biocmanager" by f1014063507 • 0
Thanks for answering. In fact, I can use the computer to install packages by "install.packages()", but the "biocmanager::install()" doesn'…
Votes
Answer: Joint disperstion estimation for DEXSeq and DESeq2
Answer: Problems to find the pvalues via rowttests
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
Annotating GRanges with TxDb gene models using plyranges
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