User: irving.jgalo23

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Posts by irving.jgalo23

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Comment: C: Error topGO printGenes
... Thanks for your time, that's how I built my Godata GOdata  <- new ("topGOdata", ontology = "CC",                allGenes = all_pvlue , geneSel = topDiffGenes,                description = "Arabidopsis_Genes", nodeSize = 10,                annot = annFUN.org, mapping = "org.At.tair.db")     Re ...
written 10 months ago by irving.jgalo230
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Error topGO printGenes
... Hi, I want to extract the enriched genes from the significative GO terms with the printGenes function. goID <- "GO:0005730" gt <- printGenes(GOdata, whichTerms = goID, chip = "org.At.tair.db", numChar = 40) But when I run the script I get the following error: Error in d ...
topgo written 10 months ago by irving.jgalo230
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Comment: C: Matrix is not full rank with Multifactorial Experiment and Time course
... Hi Michael, thanks for your answer. In this case, I want to compare the time 0 vs all the times (0 vs 15, 0 vs 45 ..... etc), to observe through time that genes change in contrast to time 0, both in cotyledons and in hypocotyls while you apply the light treatment. But I think that I have to consider ...
written 13 months ago by irving.jgalo230
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Matrix is not full rank with Multifactorial Experiment and Time course
... Hi I have a multifactorial experiment with three factors: two levels of light treatment( high and low), two levels for tissues (cotyledon and hypocotyl), and finally I have a time course with four levels (15, 45, 90, 180 including the time 0). We have 57 libraries with replicates. > coldata ...
deseq2 time course multiple factor design model.matrix written 13 months ago by irving.jgalo230 • updated 13 months ago by Michael Love20k

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