User: Levi Waldron

gravatar for Levi Waldron
Levi Waldron80
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3 years, 9 months ago
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l***********@hunter.cuny.edu

Posts by Levi Waldron

<prev • 8 results • page 1 of 1 • next >
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Answer: A: getting normalized expression values from GEO GSE files
... On Wed, Aug 27, 2014 at 4:18 PM, Maria Kesa wrote: > 2. How should I normalize the data, considering that there are multiple > platforms in the experiment? > It's not obvious from the GEO page or the paper why they used 7 platforms, but I believe they may be complementary and intended to ...
written 3.2 years ago by Levi Waldron80
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Microarray data normalization
... Depending on which Affy platform you have, you may also be able to use Frozen RMA (bioc library frma), then it doesn't matter which option you choose. On Wed, Jul 30, 2014 at 5:32 AM, Wolfgang Huber wrote: > Dear Bernarnd > > my preference would be option 2, but the first thing to do if ...
normalization go cancer probe affy written 3.3 years ago by Levi Waldron80
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Comment: C: chip removal from lumiBatch object
... When I last worked with LumiBatch objects, I found that the [, -9] method did not subset control probes data. I'm pasting a work-around I used - apologies to maintainers that I didn't think at the time to report this. lumi.subset <- function(lumibatch.obj,index){ ##---------------------------- ...
written 3.3 years ago by Levi Waldron80
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Error installing impute package
... I just noticed this problem myself - not with impute itself, but because WGCNA is not building in CRAN for Mavericks. I guess CRAN doesn't have linkable URLs, but here is the error message on the WGCNA build check for Mavericks: using R version 3.1.0 Patched (2014-06-11 r65921) using platform: x86 ...
gui impute dnacopy written 3.4 years ago by Levi Waldron80 • updated 3.4 years ago by Dan Tenenbaum ♦♦ 8.2k
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Comment: C: Microarray data analysis
... On Sun, Mar 23, 2014 at 9:40 AM, prabhakar ghorpade < prabhakar_ghorpade@yahoo.co.in> wrote: > Hello, > > Thanks for reply. I am trying to run limma with user guide instructions > but from page 11 of user guide. I am getting following error > > targets <- readTargets("ta ...
written 3.7 years ago by Levi Waldron80
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Comment: C: Microarray data analysis
... >From the http://www.bioconductor.org/help/ page, check out the "Oligonucleotide arrays" link which has example data and workflows. On Sat, Mar 22, 2014 at 11:22 AM, Sean Davis wrote: > For microarray data analysis, I would starting with the limma package. The > User Guide is a great r ...
written 3.7 years ago by Levi Waldron80
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beadarray: mRNA QC help
... Dear Abhi, it looks to me like your chips had low hybridization, based both on the low percentage of probes detected and on the low interquartile range of intensities. Fig. 2 from PMID23136189 (admittedly my publication) shows the range of IQRs for samples within several published studies using Il ...
probe ffpe written 3.8 years ago by Levi Waldron80
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Answer: A: beadarray: mRNA QC help
... Dear Abhi, it looks to me like your chips had low hybridization, based both on the low percentage of probes detected and on the low interquartile range of intensities. Fig. 2 from PMID23136189 (admittedly my publication) shows the range of IQRs for samples within several published studies using Il ...
written 3.8 years ago by Levi Waldron80

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Popular Question 3.2 years ago, created a question with more than 1,000 views. For Error installing impute package

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