User: alexvpickering

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Posts by alexvpickering

<prev • 20 results • page 1 of 2 • next >
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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 4 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 5 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 6 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 9 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 9 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 9 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 2.2 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 2.3 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 2.8 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 2.9 years ago by alexvpickering110

Latest awards to alexvpickering

Appreciated 8 months ago, created a post with more than 5 votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Popular Question 8 months ago, created a question with more than 1,000 views. For GEOquery::getGEO warning: not all columns named in 'colClasses' exist
Popular Question 23 months ago, created a question with more than 1,000 views. For RAW data in matrix: RMA normalization?
Great Question 23 months 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 2.3 years ago, created an answer that has been accepted. For A: Meta-analysis of microarrays (and RNA-seq) data
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Popular Question 3.3 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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