User: He, Yiwen NIH/CIT

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Posts by He, Yiwen NIH/CIT

<prev • 35 results • page 1 of 4 • next >
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Affy HTA 2.0 array analysis
... Hi, I am trying to analyze the affy HTA 2.0 array. I tried to create the pd.hta.2.0 package using makePdInfoPackage() in the pdInfoBuilder package, and got a message saying data type mismatch. I searched the archive and saw people with the same problem, but no solutions. Can someone please help? I ...
annotation affy written 6.1 years ago by He, Yiwen NIH/CIT360 • updated 4.4 years ago by Jason Hubbard20
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Answer: A: A question about the gage package
... Hi, I am looking into using the gage package for gene set analysis. I would like to test run it on the human diabetic muscle microarray data used in the initial description of GSEA paper. I downloaded the expression data (Diabetes_hgu133a.gct) from the Broad institute website, and also downloaded t ...
written 6.6 years ago by He, Yiwen NIH/CIT360
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A question about the gage package
... Hi, I am looking into using the gage package for gene set analysis. I would like to test run it on the human diabetic muscle microarray data used in the initial description of GSEA paper. I downloaded the expression data (Diabetes_hgu133a.gct) from the Broad institute website, and also downloaded t ...
microarray probe gage written 6.6 years ago by He, Yiwen NIH/CIT360
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Comment: C: Questions about MAplot in the oligo package
... Hi, Thank you for the explanation. That helps. I was testing a tool using the oligo package, with only 3 ST arrays, two of which are very similar (but are different hybridizations). The small sample size might have caused the median and IQR to be zero. I will test it with more samples. Thank you v ...
written 6.6 years ago by He, Yiwen NIH/CIT360
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Questions about MAplot in the oligo package
... Hi, I am using the oligo package for ST gene arrays, and I have some questions about the MAplot() function in the oligo package. This is part of my sessionInfo(): > sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) other attached packages: [1] pd.hugene.1.0.st ...
oligo written 6.6 years ago by He, Yiwen NIH/CIT360 • updated 6.6 years ago by Benilton Carvalho4.3k
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A question about MAplot in the oligo package
... Hi, I am using the oligo package for ST gene arrays, and I have some questions about the MAplot() function in the oligo package. This is part of my sessionInfo(): > sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) other attached packages: [1] pd.hugene.1.0.st ...
oligo written 6.6 years ago by He, Yiwen NIH/CIT360
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LIMMA: Help needed for limma analysis with a complex design.
... Hi, I need help with analysis using the limma package. Here is the experiment design: 20 patients, 10 on a regular diet and the other 10 on a special treatment diet. For each patient, 4 samples were obtained: day 1, before and after diet; day 6, before and after diet. Thus there are a total of 2 ...
limma written 7.0 years ago by He, Yiwen NIH/CIT360
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Help needed for limma analysis with a complex design.
... Hi, I need help with analysis using the limma package. Here is the experiment design: 20 patients, 10 on a regular diet and the other 10 on a special treatment diet. For each patient, 4 samples were obtained: day 1, before and after diet; day 6, before and after diet. Thus there are a total of 20 ...
limma written 7.0 years ago by He, Yiwen NIH/CIT360
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Need help with pdInfoBuilder package for human ST arrays
... Hi, I am trying to use the pdInfoBuilder package to build design info package for the Affy Human Gene ST 1.0 arrays. I have several questions and appreciate if someone can share their knowledge. I used R 2.11/BioC 2.6, but had the same problem with R 2.10/BioC 2.5. 1. I had to specify the coreMps ...
annotation affy oligo pdinfobuilder written 9.3 years ago by He, Yiwen NIH/CIT360
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Affy CEL file herder info
... Hi, We are trying to extract the header info in the affy CEL files, particularly the scan date and time and the scanner serial number. The affyxparser:readCelHeader and affyio:read.celfile.header function works fine for the text and binary CEL files. However when I tried them on the AGCC generated ...
affy written 9.8 years ago by He, Yiwen NIH/CIT360 • updated 9.8 years ago by Henrik Bengtsson2.4k

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Popular Question 6.1 years ago, created a question with more than 1,000 views. For Affy HTA 2.0 array analysis

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