Bioconductor Intensity

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MSnbase chromatograms intensity

updated 5.8 years ago by Laurent Gatto 1.6k • written 5.8 years ago by djshipman2011 ▴ 10

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xcms xcmsset intensity

6.7 years ago cpataki • 0

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affy exprs intensity

updated 7.0 years ago by James W. MacDonald 68k • written 7.0 years ago by elmira.amiri • 0

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affy intensity probes

updated 8.7 years ago by James W. MacDonald 68k • written 8.8 years ago by m_punisher6 • 0

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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"…

Answer: Memory issue while using "quickcluster" and "computeSumFactors" functions on sin by James W. MacDonald 68k

The obvious solution is to use cloud computing, which is likely cheaper than getting more RAM for your computer.

Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k

``` library(org.Dm.eg.db) rn <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "SYMBOL","FLYBASE") ## ensure no NA values get propaga…

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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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