User: alexvpickering

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Posts by alexvpickering

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Comment: C: Meta-analysis of microarrays (and RNA-seq) data
... Hi Paul,  Get in touch and I'll try to help you out: alexvpickering at gmail dot com. ...
written 11 months ago by alexvpickering80
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Answer: A: Meta-analysis of microarrays (and RNA-seq) data
... Hi Paul, I am the author of crossmeta, which uses the same effect-size methods as GeneMeta. The methods were modified so that genes that are only measured in a subset of studies can still be included in the meta-analysis. I chose to use an effect-size (as opposed to p-value or rank) meta-analysis m ...
written 12 months ago by alexvpickering80
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Comment: C: meta analysis of microarrays of small sample sizes
... Hi Lian, If you want to use variance filtering as part of the work flow with crossmeta I would first try to exclude only those genes that are consistently filtered by genefilter across all your esets. To do this (example data as in vignette): library(crossmeta) library(lydata) library(genefilter) ...
written 19 months ago by alexvpickering80
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Answer: A: meta analysis of microarrays of small sample sizes
... Hi Lian,  I don't think it makes sense to perform non-specific filtering for meta-analysis. If you do, genes filtered from as few as one study will be excluded from the meta-analysis because GeneMeta will only analyse genes included in all studies. This could result, for example, in the exclusion o ...
written 19 months ago by alexvpickering80
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Answer: A: Algorithm for between and within microarray normalisation (for meta-analysis).
... My recommendation is that you use the crossmeta package, which I wrote specifically for the purpose of doing cross-platform and cross-species meta-analyses of public microarray data from GEO. If you try to do it from scratch, you will run into a multitude of issues including: Annotation:  D ...
written 22 months ago by alexvpickering80
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Answer: A: Question on how to proceed and analyze 9 microarray datasets of two different pl
... I recently released the Bioconductor package crossmeta which extends the effect size meta-analysis method in GeneMeta to allow for genes that were not measured in all studies. crossmeta also automates downloading, annotating, and batch effect correction of raw data. All you need is a list of GSEs th ...
written 22 months ago by alexvpickering80
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GEOquery::getGEO warning: not all columns named in 'colClasses' exist
... I'm getting a warning message from GEOquery function getGEO (only seems to happen with GSEMatrix = TRUE).  May be a bug (I believe everything is up to date). library(GEOquery) gse <- getGEO("GSE61538", GSEMatrix=TRUE) Warning message: In read.table(file = file, header = header, sep = sep, quot ...
geoquery written 2.0 years ago by alexvpickering80 • updated 2.0 years ago by Sean Davis21k
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Answer: A: ReadAffy() Error - 2 Platforms in one file
... Bit late on the response but might be useful to someone else. Just had to solve this problem myself. Basic idea is to get each GSEMatrix, grab the sample names, and use those to load the appropriate CEL files seperately. gse_name <- "GSE5054" data_dir <- paste(getwd(), "data", sep="/") gse_d ...
written 2.1 years ago by alexvpickering80
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MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
... My data is setup as in the MetaDE vignette:  gene_tstats & gene_pvals are matrices with rownames corresponding to gene names and moderated t-statistic / p-values for each study.  gene_tstats and gene_pvals have the same column names and dimensions (20917 * 3) and no NA values (although ...
meta-analysis metade written 2.2 years ago by alexvpickering80
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[SOLVED] BUG REPORT: Ubuntu 14.04 xps Installation libcrypto.so.10
... Spent a long time trying to install xps on Ubuntu 14.04. After successful installation of ROOT (root_v5.34.24.Linux-slc6_amd64-gcc4.8.tar.gz - specific to my system as gcc4.8 and 64bit). I got this error message from running either  R CMD INSTALL xps_1.30.0.tar.gz or  source("http://bioconducto ...
xps ubuntu written 2.2 years ago by alexvpickering80 • updated 2.2 years ago by cstrato3.8k

Latest awards to alexvpickering

Popular Question 11 months ago, created a question with more than 1,000 views. For [SOLVED] BUG REPORT: Ubuntu 14.04 xps Installation libcrypto.so.10
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Scholar 12 months ago, created an answer that has been accepted. For A: Meta-analysis of microarrays (and RNA-seq) data
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Popular Question 2.1 years ago, created a question with more than 1,000 views. For [SOLVED] BUG REPORT: Ubuntu 14.04 xps Installation libcrypto.so.10

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