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R deseq2 differential gene expression help

7.0 years ago • updated 6.9 years ago fischer87 • 0

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edger differential gene expression without replicate nested design help

updated 6.9 years ago by Aaron Lun ★ 28k • written 6.9 years ago by knipehf • 0

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clusterprofiler input files error help

updated 6.2 years ago by Guangchuang Yu ★ 1.2k • written 6.3 years ago by Mataivic • 0

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limma time series help

updated 4.4 years ago by Aaron Lun ★ 28k • written 4.4 years ago by rm1238 • 0

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HELP ChIC.data PeakDetection ChipOnChipData

8 months ago • updated 7 months ago michela ▴ 20

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HELP Data

updated 9 months ago by Guido Hooiveld ★ 3.6k • written 9 months ago by mcclurejenniferc • 0

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limma help

updated 7.5 years ago by svlachavas ▴ 810 • written 7.5 years ago by libya.tahani • 0

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RNASeqData RNASeq GEO RNASeqR HELP

2.2 years ago hgalmoore • 0

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STRINGdb HELP

updated 3 months ago by Rodrigo ▴ 10 • written 15 months ago by Jessica ▴ 10

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HELP HelloRanges

updated 7 months ago by James W. MacDonald 63k • written 7 months ago by michela ▴ 20

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HELP ChIPpeakAnno

18 months ago lexi.kellington • 0

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DESeq2 HELP

3 months ago Michael • 0

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DESeq2 volcanoplot deseq HELP contrast

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help DESeq2 DESeqDataSetFromMatrix rownames

updated 12 months ago by Sanatan • 0 • written 2.1 years ago by dorina.jamniczky • 0

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help software error

updated 4.4 years ago by Martin Morgan 25k • written 4.4 years ago by mafusa20 • 0

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ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene

7 months ago michela ▴ 20

16 results • Page 1 of 1

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Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k

No, you are not losing power. The two possible limma analyses (fixed or random Subject effects) are both more powerful than the alternative…

Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20

Thanks Gordon Actually, I am working in the clinical statistics department for the last 5 years, even though a bioinformatician, and the "…

Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k

I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…

Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k

Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.

Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k

> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…

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A: Ranges from a fasta file

Answer: NA transcript values in my Txdb

Comment: Interpret plot from DiffBind

Answer: Use with_go along with other filters in getBM function

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Scholar to Mike Smith ★ 6.0k