User: tleona3

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tleona310
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Posts by tleona3

<prev • 7 results • page 1 of 1 • next >
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EDGE microarray time series analysis fit_models() ERROR
... Hi All, I'm using the bioconductor EDGE package for R to look for differentially expressed genes in a microarray time series dataset. I have a question regarding the parameters on the de_object creation using build_study {edge}. 1) How is the ind argument incorporated into the full/null model cre ...
time series microarray written 22 months ago by tleona310
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Comment: C: arrayanalysis.org custom CDF version
... Thanks Kevin, I ended up just doing it using Affy once I downloaded the specific custom CDF I wanted to use from Brain Array. For those who may have issues installing and applying the custom CDF, I've posted my script below. #Set working directory setwd("~/Desktop/mc") #Install Custom ...
written 2.1 years ago by tleona310
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arrayanalysis.org custom CDF version
... Hi all, I'm using this on-line module to do the pre-processing and QC of my .CEL microarray data. My question is quite simple, but I after looking through their documentation I cannot find an answer. When mapping to a custom CDF (say hgu133plus2_Hs_ENSG), how can I know which brain array version o ...
pre-processing quality control microarray written 2.1 years ago by tleona310
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Comment: C: Microarray experimental design and analysis; repeated measures ANOVA, MaSigPro
... Thanks for the helpful response! I agree that the design is quite complex, and unfortunately the patient time points were setup this way due to limitations in the IRB protocol. It gets a bit worse in that some of the sample time points in each group are missing as they were not run on the microarr ...
written 2.1 years ago by tleona310
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Microarray experimental design and analysis; repeated measures ANOVA, MaSigPro
... Hi All, I have a large RNA microarray dataset that I am planning to analyze, but am having difficulty deciding what statistical tests to perform or R packages to used based on the experimental design. The design is as follows: There are 21 patients who have had tissue biopsies performed in two dif ...
R statistics microarray masigpro anova written 2.1 years ago by tleona310 • updated 2.1 years ago by Kevin Blighe51k
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Comment: C: Time point microarray data correcting for batch effects
... Hi mforde84, Thanks for your response. I'm afraid I might not have been clear in my question. I was planning to use ComBat to correct for chip to chip batch effects, but based on the sample layout across chips (see original post) and my experimental question I'm looking to answer I'm worried I won' ...
written 2.2 years ago by tleona310
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Time point microarray data correcting for batch effects
... Hi All, I'm looking at an old microarray gene expression dataset and I had a question about correcting for chip to chip batch effects. The samples were run on the Affymetrix Mouse Genome 430 2.0 Array. The experimental design is the following: 3 biological replicates of both paired mouse cutaneou ...
combat microarray batch effect written 2.2 years ago by tleona310 • updated 2.2 years ago by mforde841.2k

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Popular Question 9 months ago, created a question with more than 1,000 views. For Microarray experimental design and analysis; repeated measures ANOVA, MaSigPro

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