User: Paz Tapia Ramirez

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Posts by Paz Tapia Ramirez

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Rocks cluster
... Hello, I need to install bioconductor in rocks cluster. I installed it on the master node, but on the other nodes is not installed. If anyone can help me, please. Thanks, [[alternative HTML version deleted]] ...
written 7.8 years ago by Paz Tapia Ramirez150 • updated 7.8 years ago by Vincent J. Carey, Jr.6.3k
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Comment: C: process one color microarray
... Jim, I need to do an analysis of expression differential of genes. I do not know if using M values ​​or log-ratios. Regards, > Date: Mon, 19 Sep 2011 09:06:03 -0400 > From: jmacdon@med.umich.edu > To: verotapia@alumnos.utalca.cl > CC: yong.li@zbsa.uni-freiburg.de; bioconduct ...
written 8.0 years ago by Paz Tapia Ramirez150
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load single-channel microarray
... Hi, When loading data from single channel produces a EList, and when it is 2 channel creates a MAlist. When loading the datas with package marray, Where and how to differentiate if is singe-channel or two-channel? Thanks [[alternative HTML version deleted]] ...
marray written 8.0 years ago by Paz Tapia Ramirez150
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Comment: C: process one color microarray
... Hello, when I create a design of a matrix with: cond <- factor (rep (1:4, EACH = 2)) # 2 replicates of each treatment design <- model.matrix (~ 0 + cond) colname (design) <- c ("treatment1", "treatment2", "treatment3", "treatment4") contrast <- makeContrasts (treatment2-trea ...
written 8.0 years ago by Paz Tapia Ramirez150
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makeContrast in limma package
... Hi, I don't known the argument in makeContrast function of limma package. Says: contrast <- makeContrasts("X - Y", levels=design) I known that X can be Treatment and Y the Control, but what is equivalent? some specific columns target in my target file? Thanks, Paz [[alternativ ...
written 8.0 years ago by Paz Tapia Ramirez150 • updated 8.0 years ago by Gordon Smyth38k
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Comment: C: process one color microarray
... Are one- color microarrays. 4 different treatment, one of them is control. Each treatment has 4 replicas. I need to get the differential gene expression. My target file is: "FileName" "Treatment" "GErep" "ISO_1.txt" "ISO" "1" "ISO_2.txt" "ISO" "2" "ISO_3.txt" "ISO" "3" "ISO_4. ...
written 8.0 years ago by Paz Tapia Ramirez150
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Comment: C: process one color microarray
... Hi JIM. When you say "trt1" "trt2" you mean the column GErep in the targets file ? > Date: Fri, 16 Sep 2011 13:32:30 +0200 > From: yong.li@zbsa.uni-freiburg.de > To: jmacdon@med.umich.edu > CC: verotapia@alumnos.utalca.cl; bioconductor@r-project.org > Subject: Re: [BioC] pr ...
written 8.0 years ago by Paz Tapia Ramirez150
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Comment: C: process one color microarray
... Hi Yong, What do you recommend? Best Regards, Paz > Date: Fri, 16 Sep 2011 13:32:30 +0200 > From: yong.li@zbsa.uni-freiburg.de > To: jmacdon@med.umich.edu > CC: verotapia@alumnos.utalca.cl; bioconductor@r-project.org > Subject: Re: [BioC] process one color microarray > ...
written 8.0 years ago by Paz Tapia Ramirez150
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process one color microarray
... Hello, I have a question. I'm Working with one-color microarrays . I worked in 4 conditions different and each condition I have 4 replicates. Now, my question is when I load the files to Bioconductor, I load as follows: my.filenames <- c ("Condic1_repl1.txt", " ...
normalization written 8.0 years ago by Paz Tapia Ramirez150 • updated 8.0 years ago by James W. MacDonald51k
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normalization microarray
... Hello, I need to get the normalized values ​​in a file, how I can do that?. I will normalize, but do not know how to visualize the normalized values ​​to a file. I normalized as follows: one.col <-list( R="gMeanSignal",G="gProcessedSignal", Rb="gBGMedianSignal",Gb="gProce ...
written 8.0 years ago by Paz Tapia Ramirez150 • updated 8.0 years ago by Sean Davis21k

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Popular Question 7.8 years ago, created a question with more than 1,000 views. For Error in` [. Data.frame `(obj, , columns [[a]]): undefined columns selected"

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