User: fromhj304

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fromhj30410
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Posts by fromhj304

<prev • 12 results • page 1 of 2 • next >
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FPKM normalization questions!
... Hi all, I'm having a hard time understanding a concept in bioinformatics. So right now, I'm learning FPKM values. I'm not sure why we need this value in the first place. What is importance and what does it tell you that raw count data don't? Also, why do we need to normalized the data? I don't quit ...
R bioinformatics fpkm written 2.1 years ago by fromhj30410 • updated 2.1 years ago by Aaron Lun21k
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Comment: C: adjusted p-values and p-values problems!
... Then in this case would (condition <- factor(c(rep("sample", 6), rep("control", 2)))) This work? ...
written 2.1 years ago by fromhj30410
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surrogate variable analysis using R package "sva"
... Hi all, I have RNA-Seq raw count data and I want to take rlog (regularized log transform) to run surrogate variable analysis using R package. FYI, here is my code: >source("https://bioconductor.org/biocLite.R") >biocLite("DESeq") >library(DESeq2) >dat <- read.table("TestData_09_30_ ...
sva R bioinformatics written 2.1 years ago by fromhj30410 • updated 2.1 years ago by Diego Diez730
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Comment: C: adjusted p-values and p-values problems!
... Hi Mike, I've actually used that documentation when I used DESeq2 and plotting PCA plot. My condition is: (condition <- factor(c(rep("KO1", 1), rep("KO2", 1), rep("KO3", 1), rep("KO4", 1), rep("KO5", 1), rep("KO6", 1), rep("Control1", 1), rep("Control2", 1)))) which are the samples and controls ...
written 2.1 years ago by fromhj30410
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Comment: C: adjusted p-values and p-values problems!
... I want to compare all samples, but when I run results() only KO6 and control1 are being compared. I'm not sure what makes them compare only those two. Do I need to add parameters when calling results()? ...
written 2.1 years ago by fromhj30410
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Comment: C: adjusted p-values and p-values problems!
... Hi Mike, thanks for the reply! I was simply asked to get a DEG for p-value < 0.05 or < 0.01. Without further explanation. Since I have so many genes (30,000), it makes sense that adjusted p-value would have repeated values. Is it not okay to use p-values? My understanding was that depending o ...
written 2.1 years ago by fromhj30410
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topGO for Gene Ontology and Gene Set enrichment
... Hi all, I'm trying to get Gene Ontology and Gene Set Enrichment using topGO. I'm pretty novice to bioinformatics using R, so I need your help! So from RNA-Seq raw count data (31973 genes), I used DESeq2 to get differentially expressed genes, using results(), and from there I sorted by p-values. I d ...
topgo gene ontology bioinformatics rna-seq gene set enrichment written 2.1 years ago by fromhj30410 • updated 22 months ago by Lluís Revilla Sancho420
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adjusted p-values and p-values problems!
... Hi all, I'm working with my RNA-Seq raw count data right now. I'm in the process of determining differentially expressed genes among the file, and I used DESeq2 package for R to do that. #run the DESeq pipeline dds <- DESeq(dds) #delete all the data that have total of 0 counts dds<-dds[rowSu ...
R rna-seq adjusted pvalue pvalue bonferroni written 2.1 years ago by fromhj30410 • updated 2.1 years ago by Michael Love20k
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Comment: C: Differential Gene Expression
... Thank you so much!! ...
written 2.1 years ago by fromhj30410
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Comment: C: Differential Gene Expression
... Hi thank you so much for the answer! But why did you use adjusted p-values instead of just p-values? What are their differences?   Thanks again!   ...
written 2.1 years ago by fromhj30410

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