User: nelson.s.garcia

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Posts by nelson.s.garcia

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Comment: C: [DESeq2] Extracting results based on set thresholds
... Thanks Michael! ...
written 5 months ago by nelson.s.garcia0
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Comment: C: [DESeq2] Extracting results based on set thresholds
... Thanks Michael! In my case:  log2 fold change (MLE): Mo17M vs CMLM Wald test p-value: Mo17M vs CMLM  This means that the genes with l2fc positive values are upregulated in the sample Mo17M. Is this correct? ...
written 5 months ago by nelson.s.garcia0
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[DESeq2] Extracting results based on set thresholds
... Hello, After running DESeq and filtering using alpha = 0.05 and lfcThreshold = 1 > dds <- DESeq(dds) > res.05_1 <- results(dds, alpha = 0.05, lfcThreshold = 1) > summary(res.05_1) out of 33402 with nonzero total read count adjusted p-value < 0.05 LFC > 1.00 (up)    : 964, 2.9 ...
deseq2 written 5 months ago by nelson.s.garcia0 • updated 5 months ago by Michael Love21k
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Comment: A: Importing multiple .h5 files using tximport
... Thanks. How can I create the vector? ...
written 8 months ago by nelson.s.garcia0
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Tutorial: Importing multiple .h5 files using tximport
... I am having trouble with importing kallisto files for DESeq analysis in R. I went to the tutorial website and found this:  files <- file.path(dir, "kallisto_boot", samples$run, "abundance.h5") names(files) <- paste0("sample", 1:6) txi.kallisto <- tximport(files, type = "kallisto", txOut = ...
tutorial tximport written 8 months ago by nelson.s.garcia0 • updated 8 months ago by Steve Lianoglou12k

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