User: Matthew McCall
Matthew McCall • 830
- Reputation:
- 830
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- Trusted
- Location:
- United States
- Website:
- http://mnmccall.com/
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- Google Scholar Page
- Last seen:
- 4 months, 2 weeks ago
- Joined:
- 8 years, 8 months ago
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Posts by Matthew McCall
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... You need to have replicate samples, defined by one or more grouping variables. Please take a look at the example in the qpcrImpute man page:
data(sagmb2011)
tst <- qpcrImpute(sagmb2011, groupVars="sampleType",
outform=c("Single"), batch=NULL, linkglm ...
written 4 months ago by
Matthew McCall • 830
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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 18 months ago by
Matthew McCall • 830
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... 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 19 months ago by
Matthew McCall • 830
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... 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 19 months ago by
Matthew McCall • 830
1
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... 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 19 months ago by
Matthew McCall • 830
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... 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 19 months ago by
Matthew McCall • 830
0
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... 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 19 months ago by
Matthew McCall • 830
3
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1
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... 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 23 months ago by
Matthew McCall • 830
0
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... 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 2.2 years ago by
Matthew McCall • 830
0
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... 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 2.4 years ago by
Matthew McCall • 830
Latest awards to Matthew McCall
Student
17 months ago,
asked a question with at least 3 up-votes.
For DESeq fitted values using coefficients vs mu
Centurion
17 months ago,
created 100 posts.
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: Processing several GSM from GEO database using Barcode and fRMA
Scholar
2.4 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: Strategies for fRMA on custom dataset(s)?
Scholar
4.7 years ago,
created an answer that has been accepted.
For A: frma vectors for GPL13158 (Affymetrix HT HG-U133+ PM Array Plate)?
Scholar
4.7 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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