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User: alexvpickering

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Posts by alexvpickering

<prev • 18 results • page 1 of 2 • next >
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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 14 days 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 3 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 3 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 3 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 20 months 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 22 months 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 2.3 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 2.4 years ago by alexvpickering110
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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 2.6 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 2.6 years ago by alexvpickering110

Latest awards to alexvpickering

Great Question 17 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 17 months ago, created a question with more than 1,000 views. For RAW data in matrix: RMA normalization?
Popular Question 20 months ago, created a question with more than 1,000 views. For [SOLVED] BUG REPORT: Ubuntu 14.04 xps Installation libcrypto.so.10
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Scholar 21 months ago, created an answer that has been accepted. For A: Meta-analysis of microarrays (and RNA-seq) data
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Meta-analysis of microarrays (and RNA-seq) data
Popular Question 2.8 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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