User: joseph

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joseph330
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Posts by joseph

<prev • 33 results • page 1 of 4 • next >
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Comment: C: EdgeR design question?
... Dear Gordon Thank you for your help. Following the 3.3.2 section of the user guide: #set the references targets$Age <- relevel(targets$Age, ref="Young") targets$Genotype <- relevel(targets$Genotype, ref="Wt") #set design1 design1 <- model.matrix(~ Genotype + Genotype:Age, data=targets) &g ...
written 5.4 years ago by joseph330
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EdgeR design question?
... Hi I am using edgeR to analyse an RNA-seq experiment with two factors, age (Young, Old) and genotype (Wt, Mutant). > targets            Age Genotype Sample1  Young       Wt Sample2  Young       Wt Sample3  Young       Wt Sample4  Young   Mutant Sample5  Young   Mutant Sample6  Young   Mutant Samp ...
edger written 5.5 years ago by joseph330 • updated 5.4 years ago by Gordon Smyth37k
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Failed loading Biobase
... Hi I installed R-devel-leopard.pkg (56Mb, installer incl. GUI) from http://r.research.att.com/ on my Mac. I installed core Bioconductor packages with: source("http://bioconductor.org/biocLite.R") biocLite() I got the following error when I tried to load Biobase: Please help me to solve this issue. ...
written 6.9 years ago by joseph330
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Answer: A: Failed loading Biobase
... An embedded and charset-unspecified text was scrubbed... Name: not available URL: ...
written 6.9 years ago by joseph330
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Comment: C: siggenes sam2excel Error
... Hi Holger here is my code, I also attached the data files. sumis.data = read.table("sumis.data", header = T) > sumis.data[1:3, ] Y3 Y4 O1 O2 O3 1 37 47 43 35 15 2 40 40 28 23 17 sumis.names=read.table("sumis.names", header = T) sumis.names[1:3, ] [1] chr1_829531_830948_8 chr1_834144_836446_8 ...
written 8.2 years ago by joseph330
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siggenes sam2excel Error
... Hi I get an error when I use sam2excel to export sam output: > sam2excel(sam.out, 0.1, file="sam.out.csv", n.digits = 2, what = "both", quote >= FALSE, entrez = FALSE) Error in if (all(rownames(mat.sig) != as.character(1:nrow(mat.sig)))) mat.sig <- data.frame(mat.sig, : missing value wh ...
written 8.2 years ago by joseph330 • updated 8.2 years ago by Holger Schwender900
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Comment: C: prepare data matrix for siggenes
... Hi Holger I got an Warning message when I used the data: > sam.out = sam(sumis, cl, rand = 123, gene.names = sumis.names, var.equal = >TRUE) We're doing 70 complete permutations Warning message: There are 2 variables with zero variance. These variables are removed, and their d-values are set ...
written 8.2 years ago by joseph330
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prepare data matrix for siggenes
... I am preparing data matrix for siggenes as follow: data=read.table("data.txt", skip=1, header = F) data=as.matrix(data) data[1:3, ] V1 V2 V3 V4 V5 V6 V7 V8 [1,] 0.26 0.21 0.37 0.47 0.43 0.35 0.15 0.50 [2,] 0.21 0.22 0.40 0.40 0.28 0.23 0.17 0.40 is it ok to have the defualt c ...
siggenes written 8.2 years ago by joseph330 • updated 8.2 years ago by Holger Schwender900
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Error with microRNA.org2df.fun (CORNA package)
... > tran2mir.df <- >microRNA.org2df.fun(url="http://cbio.mskcc.org/microrna_data/human_pr edictions_S_C_aug2010.txt.gz") > Error in `[.data.frame`(d, , col.old) : undefined columns selected Can you please advise on how to solve this problem? Joseph > sessionInfo() R version 2.12.1 RC ...
written 8.5 years ago by joseph330
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Comment: C: makeTranscriptDbFromUCSC: ... Error: Request-URI Too Large
... Hi I updated to rtracklayer_1.10.1, but I still get the same error. > sessionInfo() R version 2.12.0 Patched (2010-10-19 r53373) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics gr ...
written 8.7 years ago by joseph330

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