User: Adrian Johnson

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Posts by Adrian Johnson

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time series expression data
... Hi: Are there any ways or algorithms to carry out a meta-analysis of time series gene expression data sets. I know it is not an appropriate analysis since timepoints may not be comparable across experiments. However if I could choose only comparable time points (Say study1 and study 2 have common ti ...
written 6.8 years ago by Adrian Johnson330
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Comment: C: MetaArray - results - how to interpret
... Hi Rob, Thanks for your quick reply. Is there a way to select again from the list of 500 genes? Here is what I am trying to achieve: 1. I have 8 different Affy studies for Lung. 2. I have list of 200 genes related to a biological process. Some of the 200 genes are differentially expressed (using ...
written 7.0 years ago by Adrian Johnson330
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MetaArray - results - how to interpret
... Dear group, Pardon me for re-post. I am writing to seek some help in interpreting MetaArray poe.mcmc results. After running poe.mcmc, the resulting results object is a complicated result ( I have biology training and minimal statistics). I am trying to extract those genes that are consistently d ...
metaarray written 7.0 years ago by Adrian Johnson330 • updated 7.0 years ago by Rob Scharpf240
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Answer: A: poe.mcmc - metaArra non-numeric matrix extent error
... I got it worked. The answer is hidden in mergemaid function. poe.mcmc(exprs(intersection(merged)),NN=m) Sorry for another question. How to select genes differentially expressed across all datasets from poe.mcmc result? names(poeRes) [1] "alpha" "mug" "kappaposg" "kappanegg" ...
written 7.0 years ago by Adrian Johnson330
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poe.mcmc - metaArra non-numeric matrix extent error
... Hi: I am trying to replicate the code in metaArray package. The merged object after mergeExprs does not seem to work for poe.mcmc. Could anyone help me understand where the problem exist. Thanks in advance. > poe.mat <- poe.mcmc(merged,M=1000) Error in matrix(0, GG, TT) : non-numeric matrix ...
mergemaid metaarray written 7.0 years ago by Adrian Johnson330
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how to analyze
... dear group: is there any work flow for analyzing microRNA affy data using bioconducor packages. thanks -adrian ...
affy microrna written 7.9 years ago by Adrian Johnson330
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cox PH model - KM curve
... Dear group: I have gene expression data matrix (after RMA) as a matrix. In another table (as data frame) I have survival data. I have 25 genes for which I want to plot a Kaplan-meier curves based on cox model for these 25 genes. Is there a workflow to do this analysis. I tried phenoTest, however I d ...
survival phenotest written 8.3 years ago by Adrian Johnson330 • updated 8.3 years ago by Heidi Dvinge2.0k
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Affymetrix 250K SNP aCGH
... Dear group: I have over 280 Affy 250K SNP chip data studied for aCGH. What are the bioconductor modules that are necessary for normalization and finding regions of interest. Since the number of chips is very high, I also wonder what if R is not highly suitable for normalization due to memory issu ...
acgh snp normalization affy written 8.5 years ago by Adrian Johnson330 • updated 8.5 years ago by Djork Clevert210
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mapping coverage
... hi : has any one tried to graphically represent coverage data from capture sequencing on a chromosome. would you please share what packages you used to represent coverage graphically. thanks Adrian. ...
coverage written 8.7 years ago by Adrian Johnson330 • updated 8.7 years ago by Martin Morgan ♦♦ 23k
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package help
... Hello group, what bioconductor packages do you suggest to use for nimblegen promoter tiling arrays (NimbleGen Oligonucleotide promoter tiling array (2005-03-31_MM5) ). These chips were used on identifying methylated regions of genome using MeDIP method. Thank you. sincerely, Adrian ...
written 9.0 years ago by Adrian Johnson330 • updated 9.0 years ago by Wolfgang Huber13k

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Popular Question 12 months ago, created a question with more than 1,000 views. For gene expression data followup
Popular Question 2.9 years ago, created a question with more than 1,000 views. For cummerbund how to get matrix for csheatmap

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