User: R

gravatar for R
R40
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Germany
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3 months, 3 weeks ago
Joined:
5 years, 10 months ago
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r**********@gmail.com

Posts by R

<prev • 12 results • page 1 of 2 • next >
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Normalize a gene using lib size from another matrix
... I would like to take out raw counts from gene X from matrix A, and use the lib-size and norm-factors from a DGEList-object based on matrix B. How do I calculated the normalized expression of gene X? Thanks,   ...
limma written 3 months ago by R40
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Limma design matrix
... I have data with Treated and Control and three time-groups within each. I want to compare across the time-groups for Treated vs Control. How do I set up my desing matrix?     groupTC = c("C","C","C","C","C","C","T","T","T")     groupTC_Time = c("Early","Early","Mid,"Mid","Late,"Late","Early","Earl ...
limma design matrix written 4 months ago by R40 • updated 4 months ago by Gordon Smyth35k
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edgeR design matrix
... I have a tumor vs normal experiment. I have 48 samples of tumor and 48 of normal for the same patient. The samples are of different sex, male and female. How do I include sex as a paramenter in the analysis. This is my current setup group <- colnames(df.iso.mm2) group[grep("\\dR", colnames(df ...
limma edger written 3.0 years ago by R40 • updated 3.0 years ago by svlachavas610
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print matrix from EdgeR that are normalized by cpm and by spike-in
...     I have a small RNA data set and I want to create a matrix that is normalized based on cpm and also normalized onto my spike-in control expression. What is the best way to do this? d.RNA <- edgeR::DGEList(counts = round(counts), group=group) d.Spike <- edgeR::DGEList(counts = s)   ...
edger written 3.2 years ago by R40 • updated 3.2 years ago by James W. MacDonald47k
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Comment: A: Fitted values from EdgeR
... Dear Gordon. What is the best way to get out cpm values when I use lib.size from my libraries and norm.factors from my spike-ins. Please see pipeline below:  s=spike-ins counts=miRNAs     s <- read.delim("exprs.txt", sep="\t", check.names=FALSE) df.mdp <- read.delim("miRNAs_expressed_all ...
written 3.2 years ago by R40
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Detect global differences in miRNA expression between tumor and normal using spike-ins
... I have sequences 96 samples, 48 from tumor and 48 from normal tissue. I want to check if the miRNAs in the tumor samples are globally down-regulated compared to normal samples. I was thinking of comparing the median expression of all the tumor libraries to the median of all the normal libraries.  W ...
sequencing mirna limma edger written 3.2 years ago by R40 • updated 3.2 years ago by Aaron Lun21k
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Comment: A: Fitted values from EdgeR
... Thanks! So what are the fitted values then? ...
written 3.2 years ago by R40
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Fitted values from EdgeR
... Hi all,  I wonder of the values in lrt$fitted.values are cpm normalized values? des <- model.matrix(~KRAS) fit <- glmFit(y2, des) lrt <- edgeR::glmLRT(fit)   ...
edger R written 3.2 years ago by R40
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limma ebayes design
... I have never worked with array-data before and I have som basic question on my setup. I have normalized data in a time series with two replicates. *my samples: * colnames(hela.bc) [1] "I.0h" "I.1h" "I.2h" "I.3h" "I.6h" "I.9h" "I.12h" "I.15h" "I.18h" "I.21h" "I.24h" "II.0h" [13] "I ...
limma written 3.9 years ago by R40 • updated 3.9 years ago by James W. MacDonald47k
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Comment: C: edgeR adding RefSeq IDs
... Thanks guys, it worked. My code also worked if I justed changed [,0:1] to [,1:1]. I will try your suggestion Kasper. On Mon, Oct 21, 2013 at 5:24 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > Small comment on Jim's script > > > On Mon, Oct 21, 2013 at 10:50 ...
written 4.9 years ago by R40

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Popular Question 3.0 years ago, created a question with more than 1,000 views. For Fitted values from EdgeR

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