User: vas

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vas40
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Posts by vas

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Comment: C: Including technical and biological replicates in Limma block analysis?
... > print(Sample)   [1] "DMSO.1"   "DMSO.3"   "DMSO.2"   "DMSO.4"   "DMSO.6"   "DMSO.5"   "CH1.5.1"    [8] "CH1.5.2"  "EE75.3"   "EE75.1"   "EE75.2"   "EE75.6"   "EE75.4"   "EE75.5"    [15] "CH1.3"    "CH1.1"    "CH1.2"    "CH1.4"    "CH1.6"    "CH1.5"    "ND4.2"     [22] "ND4.3"    "ND4.1"    "ND4 ...
written 4.9 years ago by vas40
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Comment: C: Including technical and biological replicates in Limma block analysis?
... > print(y) An object of class "EList" $source [1] "illumina" $E           DMSO_H1   DMSO_H3   DMSO_H2   DMSO_H4   DMSO_H6   DMSO_H5  CH1.5_H1 6450255  4.903814  4.709843  4.605154  4.349392  4.627624  4.747999  4.525305 6370619  4.787750  4.658187  6.334636  6.976980  4.537049  4.834669  4.5135 ...
written 4.9 years ago by vas40
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Comment: C: Including technical and biological replicates in Limma block analysis?
... Hi Aaron, I tried to create the EList as you mentioned with the command  y <-maqc.norm.filt But It seems treat and pair factors carrying no information from the target file. I dont know if I should create the new Elist object with the following command to have the target information y <- ...
written 4.9 years ago by vas40
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Comment: C: Including technical and biological replicates in Limma block analysis?
... Dear Aaron. This is the output from sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin13.1.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  [1] splines   parallel  stats4    stats     graphics  grDevices  [7] util ...
written 4.9 years ago by vas40
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Comment: C: Including technical and biological replicates in Limma block analysis?
... Dear Aaron, This is the output from traceback() 5: subsetListOfArrays(object, i, j, IJ = IJ, IX = IX, I = I, JX = JX) 4: `[.EList`(x, , !d) 3: x[, !d] 2: avearrays.EList(y, ID = Sample) 1: avearrays(y, ID = Sample) ...
written 4.9 years ago by vas40
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Answer: A: Including technical and biological replicates in Limma block analysis?
... Dear Aaron, This is the output from traceback() 5: subsetListOfArrays(object, i, j, IJ = IJ, IX = IX, I = I, JX = JX) 4: `[.EList`(x, , !d) 3: x[, !d] 2: avearrays.EList(y, ID = Sample) 1: avearrays(y, ID = Sample) ...
written 4.9 years ago by vas40
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Comment: C: Including technical and biological replicates in Limma block analysis?
... Dear Gordon, I am facing the following error. y2 <- avearrays(y, ID=Sample) Error: argument "i" is missing, with no default Please help me to solve this error. Thanks in advance ...
written 4.9 years ago by vas40
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Comment: C: Including technical and biological replicates in Limma block analysis?
... (Repeated Targets file as given above) ...
written 4.9 years ago by vas40 • updated 4.9 years ago by Gordon Smyth39k
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Including technical and biological replicates in Limma block analysis?
... Hi I have a question regarding the Limma code. I have control samples (6 biological replicates, and each of the inturn have a technical replicate), I need to include all of them (12 samples) in contrast analysis. Targets file: Sample        Block        Treatment Control11        1             C ...
microarray limma linear model paired block written 4.9 years ago by vas40
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Code for Block analysis in limma.
... Hi everyone, I am new to microarray data analysis. Please evaluate the following code for block analysis in Limma and let me know about whether this code is appropriate??. library(limma) eset<-read.table("RMANormData_apap.txt") design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3,4,4,4,5, ...
microarray limma written 8.3 years ago by vas40

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Student 3.9 years ago, asked a question with at least 3 up-votes. For Including technical and biological replicates in Limma block analysis?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Including technical and biological replicates in Limma block analysis?

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