User: erwan.scaon

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Posts by erwan.scaon

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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 12 days ago by erwan.scaon0
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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 13 days ago by erwan.scaon0
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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 3 months ago by erwan.scaon0 • updated 3 months ago by Michael Love24k

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