User: alexvpickering

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Posts by alexvpickering

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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 3.1 years ago by alexvpickering110
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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 3.2 years ago by alexvpickering110
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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 3.3 years ago by alexvpickering110 • updated 3.3 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 3.5 years ago by alexvpickering110
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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 3.6 years ago by alexvpickering110
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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 3.6 years ago by alexvpickering110 • updated 3.6 years ago by cstrato3.9k
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Comment: A: neqc normalization results in bimodal histogram of expression values
... I think I figured this one out (bi-modality is perhaps to be expected - see here). It seems to be quite a common observation with RMA normalized expression data (neqc is very similar to RMA). ...
written 3.6 years ago by alexvpickering110
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neqc normalization results in bimodal histogram of expression values
... I am using neqc to normalize (bg correct, quantile normalize, and log2 transform) Illumina microarray data downloaded from GEO but am getting results that I am suspicious of. I do not have access to the negative control probe files but do have access to Detection P values (GSE39313 and GSE49000).  A ...
microarray limma illumina neqc written 3.6 years ago by alexvpickering110 • updated 3.6 years ago by Gordon Smyth38k
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Comment: C: RAW data in matrix: RMA normalization?
... Is there an appropriate normalization algorithm for cDNA arrays that will allow me to compare samples (and that keeps values as intensity measures)? I am using the characteristic direction approach to differential expression and was advised by the developers to use intensity measures (as opposed to ...
written 3.7 years ago by alexvpickering110
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RAW data in matrix: RMA normalization?
... I'm doing some analysis on GSE7829. The data supplied in the GSE Matrix has been processed by Z-normalization (instead of the more common RMA). The raw intensity values are also available  in the GSE SOFT "RAW" column and I would like to RMA-normalize these raw values. How do I approach this (the CE ...
affy rma raw expression written 3.7 years ago by alexvpickering110 • updated 3.7 years ago by James W. MacDonald51k

Latest awards to alexvpickering

Appreciated 9 months ago, created a post with more than 5 votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Popular Question 9 months ago, created a question with more than 1,000 views. For GEOquery::getGEO warning: not all columns named in 'colClasses' exist
Popular Question 2.0 years ago, created a question with more than 1,000 views. For RAW data in matrix: RMA normalization?
Great Question 2.0 years ago, created a question with more than 5,000 views. For [SOLVED] BUG REPORT: Ubuntu 14.04 xps Installation libcrypto.so.10
Popular Question 2.2 years ago, created a question with more than 1,000 views. For [SOLVED] BUG REPORT: Ubuntu 14.04 xps Installation libcrypto.so.10
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Scholar 2.4 years ago, created an answer that has been accepted. For A: Meta-analysis of microarrays (and RNA-seq) data
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Popular Question 3.4 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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