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How to read OSCA book?
BIOCON
OSCA
Bioconductor
8 months ago
zr
• 0
1
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2
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574
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WARNING: No Bioconductor dependencies detected.
Bioconductor
Biocon
8 months ago
katja.danielzik
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2
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1
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1.3k
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limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor
biocon
limma
updated 19 months ago by
Gordon Smyth
52k • written 19 months ago by
ningyuan
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1.2k
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Job:
Bioinformatician at MiroBio, Oxford, UK
Transcriptomics
Bioconductor
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Biocon
4.2 years ago
m.jackson
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3
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1.4k
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News:
Bioconductor code of conduct
biocon
code-of-conduct
Bioconductor
updated 4.3 years ago by
Lluís Revilla Sancho
▴ 760 • written 4.3 years ago by
Laurent Gatto
1.6k
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Answer: Heatmap of rnaseq data with z-score scale
by
James W. MacDonald
68k
Without including the row names for the heatmap, it's impossible to know if the directionality is switched or not. Do note that the orderin…
Comment: Heatmap of rnaseq data with z-score scale
by
giovanna
• 0
![Figure1][1]![Figure2][2] [1]: /media/images/d62918c5-2886-44ae-930d-91d292c3 [2]: /media/images/421df232-8a9c-4016-bc4a-431ca57a
Comment: parameters of filterByExpr
by
caroline.zanchi
▴ 10
Ah yes sorry :) But then I still do not understand why is it that on the plot I attached, the gene definitely has non-0 counts in less than…
Answer: Typo in the help of lmFit()
by
Gordon Smyth
52k
Thanks for the heads-up. > The _Details_ in the documentation of lmFit() still says that the default correlation is 0.75 Yes, you're righ…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
by
caroline.zanchi
▴ 10
Thank you ! ![enter image description here][1] In the end I did ```r rn2 <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "GENENAME"…
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Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
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