User: erwan.scaon

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erwan.scaon10
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Posts by erwan.scaon

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Comment: C: More Info on results names
... [This][1] might be a good read [1]: https://rpubs.com/ge600/deseq2 ...
written 6 weeks ago by erwan.scaon10
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Comment: C: Boruta and mtry parameter
... I did not take into account that it wasn't a bioconductor package, sorry for that. The question was forwarded to the author (Miron B. Kursa) of the package, who kindly replied (it did solve my issue). This question may thus be closed or deleted if it doesn't belong here. Otherwise I will post the ...
written 8 weeks ago by erwan.scaon10
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Boruta and mtry parameter
... Dear all, I am using the [Boruta][1] package and want to input non-default parameter values for ntree and mtry. From what I read in the [vignette][2], I understood that it is possible to pass these parameters to [ranger][3] (random forest implementation internally called by Boruta) : > You can ...
random forest boruta mtry ranger written 8 weeks ago by erwan.scaon10 • updated 8 weeks ago by Martin Morgan ♦♦ 23k
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Comment: C: Contrast for DESeq2 design with interaction and blocking factor
... Thanks for your reply, Using DESeq2 version 1.22.2 meta$group <- factor(paste0(meta$Extraction, meta$Prelevement)) design <- ~ NS + group dds <- DESeqDataSetFromMatrix(countData = data, colData = meta, design = design) sizeFactors(dds) <- res$GMPR dds <- estimate ...
written 10 weeks ago by erwan.scaon10
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Contrast for DESeq2 design with interaction and blocking factor
... Dear community, I am trying to perform a differential abundance analysis on 16S data using DESeq2. **The metadata is as follow** : "Prelevement" : 2 types (P1, P2) "Extraction" : 3 types (E1, E2, E3) "NS" : Corresponds to donnor ID. Each donnor (10) had 6 samples, one for each case (P1 x E1, P1 ...
deseq2 written 10 weeks ago by erwan.scaon10
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Applying external size factors to a dds did not yield expected results
... Dear community, I am using an "external" normalization method (not available in DESeq2) to obtain size factors for each sample in my dataset. Obtained size factors : sfGMPR >sfGMPR >V10T0 : 0.8564351 >V10T14 : 0.9745389 >V11T0 : 1.2577104 >V11T14 : 1.1482669 > ... ...
normalization deseq2 size factors written 5 months ago by erwan.scaon10 • updated 5 months ago by Michael Love24k

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