User: alexvpickering

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Posts by alexvpickering

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Comment: C: lpsymphony compilation trouble
... Solution from Mark worked for me as well with lpsymphony_1.11.0.tar.gz ...
written 6 months ago by alexvpickering110
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Comment: C: Algorithm for between and within microarray normalisation (for meta-analysis).
... Hi Kaouther, I don't think that will work. There has to be both control and test samples within each study. ...
written 7 months ago by alexvpickering110
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Answer: A: Meta-analysis of RNAseq data
... [RNA Meta Analysis][1] allows you to run meta-analyses that include both RNAseq and microarray studies. It currently includes ~8,000 RNAseq studies and 27,584 microarray studies. You can't currently add your own data. [1]: http://rnama.com ...
written 8 months ago by alexvpickering110
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Comment: C: Remove NaN from a list or replace NaN with a value.
... Hi Morteza, Yes, the analysis is still valid. The difference is that all contrasts are used to perform a single meta-analysis. If sources are added, then separate meta-analyses are performed for contrasts belonging to each source as well as for all contrasts. This would be useful if you want to do ...
written 11 months ago by alexvpickering110
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Comment: C: Remove NaN from a list or replace NaN with a value.
... Hi Morteza, I wasn't able to reproduce the error so I'm guessing it is a bug that has been fixed. Please download the latest version from github and try again. You should be able to do this with devtools::install_github('alexvpickering/crossmeta') or remotes::install_github('alexvpickering/crossmet ...
written 11 months ago by alexvpickering110
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Comment: C: Remove NaN from a list or replace NaN with a value.
... The error is occuring inside fdrtool::fdrtool but I don't know why. If you can share a reproducible example I'll track it down. ...
written 11 months ago by alexvpickering110
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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 2.3 years ago by alexvpickering110
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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 2.5 years ago by alexvpickering110
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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 3.0 years ago by alexvpickering110
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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 3.0 years ago by alexvpickering110

Latest awards to alexvpickering

Appreciated 10 months ago, created a post with more than 5 votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Popular Question 10 months ago, created a question with more than 1,000 views. For GEOquery::getGEO warning: not all columns named in 'colClasses' exist
Popular Question 2.1 years ago, created a question with more than 1,000 views. For RAW data in matrix: RMA normalization?
Great Question 2.1 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 2.3 years ago, created a question with more than 1,000 views. For [SOLVED] BUG REPORT: Ubuntu 14.04 xps Installation libcrypto.so.10
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Scholar 2.5 years ago, created an answer that has been accepted. For A: Meta-analysis of microarrays (and RNA-seq) data
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Popular Question 3.5 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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