Showing : nanostringdiff • reset
3
votes
2
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R NanoStringDiff: DE analysis, from 2 group comparison method how "logFC" generated?
Nan NanoStringDiff
29 days ago • updated 28 days ago choijamts • 0
2
votes
4
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582
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Why NanoStringDiff package so slow?
NanoStringDiff NanoString nCounter DE analysis
updated 9 weeks ago by ▴ 20 • written 24 months ago by ▴ 30
0
votes
0
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88
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NanoStringDiff - housekeeping genes variation
NanoStringDiff
4 months ago YM • 0
1
vote
1
reply
169
views
NanoStringDiff Not Recognized as Numeric
Bioconductor Transcriptomics NanoStringDiff
updated 9 months ago by 1.5k • written 9 months ago by ▴ 10
1
vote
7
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219
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NanoStringDiff glm.LRT not finishing after 20 hours
NanoStringDiff
18 months ago stephen.pollo • 0
0
votes
2
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215
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NanoStringDiff correction for variation between patient
NanoStringDiff GLM Gene expression
updated 23 months ago by 57k • written 23 months ago by • 0
1
vote
2
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402
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NanoStringDiff counts not numeric
NanoStringDiff
updated 2.2 years ago by 57k • written 2.2 years ago by ▴ 10
1
vote
6
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789
views
How to access normalized data in the NanoStringDiff package?
nanostringdiff nanostring NanoStringDiff
updated 3.2 years ago by 57k • written 3.2 years ago by ▴ 130
0
votes
0
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662
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring NanoStringDiff design and contrast matrix differential gene expression ncounter
4.0 years ago c.kohler • 0
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Answer: tximeta countsFromAbundance for downstream analysis by Michael Love 33k
The counts will not be closely correlated to the TPM across genes, because the gene length is included in the gene count but not in the TPM…
Answer: DESeq2 - understanding intercept and contrasts by Michael Love 33k
For questions on setting up the statistical design and contrasts, I recommend to consult with a local statistician or someone familiar with…
Answer: Interaction terms and selection of coef in normal and shrunk results by Michael Love 33k
Please see the diagram in the vignette on interactions, but for further questions on setting up the design, I recommend to consult with a l…
Answer: about baseMean in DEseq2 by Michael Love 33k
More information about the columns is here: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#access-…
Answer: DESeq2, what to do when controls are 7 times more abundant than treatments by Michael Love 33k
I generally recommend your option 2 here: filtering out genes unless they are minimally expressed in the lowly sequenced condition. This is…
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