Showing : expression • reset
5
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Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
2.9 years ago • updated 2.7 years ago mohammedtoufiq91 ▴ 10
0
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0
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767
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
3.0 years ago Jonathan • 0
0
votes
1
reply
1.6k
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Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 4.1 years ago by ▴ 90 • written 4.1 years ago by ▴ 10
1
vote
1
reply
1.7k
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Table expression data from GEO file
GEO expression GEOquery
updated 5.3 years ago by ★ 3.4k • written 5.3 years ago by • 0
1
vote
9
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2.9k
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Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs RNA-Seq Isoforms DTU expression
updated 6.1 years ago by ▴ 20 • written 6.1 years ago by • 0
1
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2
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1.1k
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Two factors design with DESEq2
deseq2 genes expression
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
7
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3
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4.5k
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Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 6.4 years ago by ★ 29k • written 6.4 years ago by ▴ 10
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6
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1.9k
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variancePartition - testing for individuals
variance formula expression
updated 6.6 years ago by ▴ 280 • written 6.6 years ago by ▴ 30
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0
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1.9k
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Job: Research Associate, Cambridge, UK - Oesophageal Cancer ICGC project
job sequencing methylation expression Job
10.5 years ago Andy Lynch ▴ 120
6
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5
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2.2k
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Limma ebayes returns a list with Affy pd.hugene.2.0.st arrays
ebayes expression affymetrix pd.hugene.2.0.st limma
updated 10.6 years ago by 52k • written 10.6 years ago by ▴ 200
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Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Your approach 1 is a bad idea. Subtracting the gene counts won't do what you want to do. I would personally check to see if there is any…
Comment: Can NanoString data be analyzed using DESeq2? by James W. MacDonald 68k
You can always discard, although you can also retain them to check for unexpected differences.
Comment: DESeq2 on NanoString Data by Michael Love 43k
Yes, if I discern a batch from EDA including looking at PCs, sample correlations, etc. It is close to SVA, we discuss both in the workflow…
Comment: DESeq2 on NanoString Data by thkapell ▴ 10
Thanks Michael. To this end, do you routinely use RUV or only when you detect a batch? It looks like it works in a similar fashion to SVA w…
Comment: Can NanoString data be analyzed using DESeq2? by thkapell ▴ 10
Thank you. I agree with your thoughts about the similarities of NanoString with RNA-seq. NanoString though, also has positive, negative pro…
Votes
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
Comment: Are voomByGroup and voomLmFit compatible?
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