User: Yong Li

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Yong Li190
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Posts by Yong Li

<prev • 19 results • page 1 of 2 • next >
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Comment: C: process one color microarray
... Hi Paz, hi Jim, I think there is a problem here. Jim, you have given detailed explanation of making design matrix and do various comparisons, but they are based on the assumption that the input given to lmFit is log expression values from one color array. The problem is that, based on Paz's code, i ...
written 8.1 years ago by Yong Li190
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Answer: A: limma::read.maimages on different chips
... Dear Brent, as no one has answered your e-mail so I will have a try. As to your first question of how to read in and normalize data from different chips together, these recent posts might be of help: https://stat.ethz.ch/pipermail/bioconductor/2011-August/040726.html https://stat.ethz.ch/pipermai ...
written 8.2 years ago by Yong Li190
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Answer: A: identity of Agilent files
... Dear Andreas, in the FEPARAMS Table (the first of the three) in the Agilent txt files there is a field named FeatureExtractor_PatternName, which is the Agilent pattern file name. It contains information like "Agilent-021169". The 021169 is the Agilent design ID, with this design ID we know which de ...
written 8.3 years ago by Yong Li190
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Comment: C: Working with Agilent 4X44k array,two color experiment
... Hello Sean, the the Agi4x44Preprocess package is only for one color Agilent arrays. I also think the limma package is the right choice as it should do the job for two color Agilent arrays. Best regards, Yong Sean Davis wrote: > On Tue, Jun 21, 2011 at 6:28 AM, Srikanth Manda Srinivas > wro ...
written 8.3 years ago by Yong Li190
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Answer: A: LIMMAing normalized and background corrected MA-data derived by a text file
... Dear Christine, the function read.maimages gives you a RGList. To convert RGList to MAList, the functions normalizeBetweenArrays can be used. You can use method="none" when calling the function to omitting any normalizations. For more details type help(normalizeBetweenArrays) in your R session. Be ...
written 8.3 years ago by Yong Li190
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limma design problem with a two color dataset
... Dear list, I am analyzing a two color microarray dataset using limma. The dataset is from ArrayExpress database (accession number E-MEXP-1949). The samples include 4 mutants (rcd11, rcd13, rcd14 and sro11) and wild- type Col0. For the 4 mutants there are 4 biological replicates each. For Col0 there ...
microarray normalization limma arrayexpress written 8.6 years ago by Yong Li190
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Comment: C: package for collapsing probe id to entrezid or gene symbols
... Hi Wendy, for something like this the function aggregate should do the job. type ?aggregate in R for more details. Yong Li Wendy Qiao wrote: > Thank you, James. > > Sorry, I did not make my question clear. > > What I meant is that, on a chip, there are multiple probes for the sam ...
written 8.6 years ago by Yong Li190
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Comment: C: Agilent annotation package for Drosophila
... Hi Clement, just want to add that you can get all the annotation files for Agilent arrays at the Agilent eArray web site (https://earray.chem.agilent.com/). Regards, Yong Marc Carlson wrote: > Hi Clement, > > We don't presently have any Agilent annotation packages for fly, but if > yo ...
written 8.8 years ago by Yong Li190
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Ringo for Nimblegen ChIP-chip data in GEO
... Dear all, I wanted to re-analyze a ChIP-chip dataset in GEO. Because it was from Nimblegen I thought Ringo is a good option. Although the raw data in GEO are not in the form as mentioned in the Ringo documentation, I have managed to read in the data with read.maimages and made a RGlist, then did so ...
normalization ringo written 9.0 years ago by Yong Li190 • updated 9.0 years ago by Wolfgang Huber13k
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Comment: C: Rgraphviz
... Hi Bhaskar, just want to add that I got the same error as you and following Martin's procedure in that e-mail the problem is fixed. Yong Martin Morgan wrote: > On 06/09/2010 10:58 PM, Bhaskar Dutta wrote: >> Hi, >> >> I am trying to use Rgraphviz package from Bioconductor. Af ...
written 9.4 years ago by Yong Li190

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