User: okna0215

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okna02150
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Posts by okna0215

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Comment: C: pathview produce 3 output files : what are they?
... Yes it is bioconductor package. According to manual : 1. hsa00040.pathview.png : original KEGG pathway map 2. hsa00040.png (some are colored in green) : layered map with given values (foldchanges) 3. hsa00040.xml : data file ...
written 27 days ago by okna02150
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pathview produce 3 output files : what are they?
... Hello all. Pathview produces 3 output files with the following command : pathview(gene.data = foldchanges, pathway.id = '00040', speices = 'hsa', same.layer = F) 1. hsa00040.pathview.png (this plot have red or green colors (representing foldchanges)) 2. hsa00040.png (some are colored in gree ...
pathview rna-seq written 6 weeks ago by okna02150
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Comment: C: DESeq2 rlogTransformed count data have negative values. Why are they negative?
... Thank you i.sudbery. Your explanation is understandable. Now I have no doubt. :) ...
written 9 weeks ago by okna02150
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Comment: C: DESeq2 rlogTransformed count data have negative values. Why are they negative?
... Thank you for kind reply. Do you mean, when counts are normalized, there would be numbers less than 1 (0 < x < 1). Then these numbers will be log transformed as minus values? As far as I understand, deseq() performs normalization of counts, and I can get normalized count values(FPKM) through ...
written 9 weeks ago by okna02150
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DESeq2 rlogTransformed count data have negative values. Why are they negative?
... Hello all. I am running RNA-seq R script and my goal is to get rlogTransformed count data. But in rlogTransformed count data : some are negative values. Does anyone know why the numbers come like this? Please give me kind explanation of this. Here is my script : countdata <- read.table("al ...
R rna-seq written 10 weeks ago by okna02150

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