User: Matthew McCall

gravatar for Matthew McCall
Reputation:
820
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Trusted
Location:
United States
Website:
http://mnmccall.com/
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Google Scholar Page
Last seen:
5 months, 2 weeks ago
Joined:
7 years, 8 months ago
Email:
m******@gmail.com

Posts by Matthew McCall

<prev • 100 results • page 1 of 10 • next >
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Answer: A: HG-U219 vectors for fRMA?
... Hi Sarah, Unfortunately, precomputed fRMA vectors don't exist for HGU219. You could try making them yourself using the frmaTools package.  Best, Matt ...
written 6 months ago by Matthew McCall820
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Answer: A: hgu133plus2hsentrezgcdf or hgu133ahsentrezgcdf packages not installing
... You can use the entrez gene remapped CDFs with frma; however, I’m several versions behind the Brain Array folks. If you look at the version field in the frozen parameter vector object, it will tell you the corresponding alternative CDF version to use.  ...
written 6 months ago by Matthew McCall820
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Comment: C: How to create vectors (makeVectorsAffyBatch) , using own cdf
... You would create an R package in the standard way. See for example:  Hadley Wickham's book: http://r-pkgs.had.co.nz/ And the BioC package guidelines: http://bioconductor.org/developers/package-guidelines/ Also any of the current frmavecs packages can serve as a useful template.  ...
written 7 months ago by Matthew McCall820
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Answer: A: How to create vectors (makeVectorsAffyBatch) , using own cdf
... The error message is telling you that it is looking for the package version of your cdf and not finding one. This is likely because you created the cdf environment but not a package. makeVectorsAffyBatch wants a package so that it can check that when you run frma on new data it was read in using the ...
written 7 months ago by Matthew McCall820
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Comment: C: How to normalize mouse gene 1.0st arry using frma?
... Guido is correct that the bottleneck is manual curation of public data and estimation of the frozen parameter vectors. For newer platforms, there may simply not be enough public data available yet. I aim for 1000 samples across 200 experiments. I do keep a mental tally of requests for frmavectors fo ...
written 7 months ago by Matthew McCall820
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Comment: C: Help running the nondetects::qpcrImpute on my data?
... Please take a look at the example in the qpcrImpute man page: data(oncogene2013) tst <- qpcrImpute(oncogene2013, groupVars=c("sampleType","treatment"), outform="Param") You need to specify which samples are replicates using the groupVars argument.  Matt ...
written 7 months ago by Matthew McCall820
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Answer: A: Processing several GSM from GEO database using Barcode and fRMA
... Hi Diana, The first step is to access the data. The GEOquery package provides a way to do this from within R. Alternatively, you can download the CEL files from GEO yourself and read them into R using the affy package. This will produce an AffyBatch object similar to the AffyBatchExample object you ...
written 11 months ago by Matthew McCall820
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Answer: A: Minimum number of genes to use R package "nondetects"
... You need to have enough genes (and samples) to get a decent estimate of the missing data mechanism. This package is designed for qPCR data (not microarrays). The 3 example data sets included with the package should provide a sense of the size / type of data sets that can be used.  ...
written 14 months ago by Matthew McCall820
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Comment: C: fRMA normalization for Mouse Gene 2.1 ST Array
... As an R novice, I would not recommend undertaking the creation of your own frma vectors. It can be a fairly involved process, especially when you're dealing with a new platform. However, if you decide to proceed, I would start with this paper: http://www.biomedcentral.com/1471-2105/12/369 And then ...
written 16 months ago by Matthew McCall820
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Answer: A: fRMA normalization for Mouse Gene 2.1 ST Array
... Unfortunately, there are not frma vectors made for this platform. You could make your own frma vectors or use a related preprocessing algorithm (e.g. rma). ...
written 16 months ago by Matthew McCall820

Latest awards to Matthew McCall

Scholar 16 months ago, created an answer that has been accepted. For A: Strategies for fRMA on custom dataset(s)?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Processing several GSM from GEO database using Barcode and fRMA
Scholar 2.7 years ago, created an answer that has been accepted. For A: Strategies for fRMA on custom dataset(s)?
Scholar 3.7 years ago, created an answer that has been accepted. For A: frma vectors for GPL13158 (Affymetrix HT HG-U133+ PM Array Plate)?
Scholar 3.7 years ago, created an answer that has been accepted. For A: frma vectors for GPL13158 (Affymetrix HT HG-U133+ PM Array Plate)?

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