User: Jean Yee Hwa Yang

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Posts by Jean Yee Hwa Yang

<prev • 92 results • page 1 of 10 • next >
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Answer: A: table2html problem
... Hi, You need to use the function "mapGeneInfo" to build a mapping between the column names of your data.frame object and the website you wanted to map it to. For example, if you have the following R object "selgene" being a data frame with the following info: Name GeneBank SMDID test AA176 ...
written 12.4 years ago by Jean Yee Hwa Yang920
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Answer: A: question about reading data into marray package
... Hi Yanqin, Assuming you have no header infomration you want to skip, can you try the following command strsplit(readLines(fnames[1], n=1), split="\t") and check if you enter the name of the columns correctly in the argument. You can also add skip = 0 in the call and see if it works. Cheers YH ...
written 12.7 years ago by Jean Yee Hwa Yang920
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Answer: A: reading arrays image analysed with spot
... Hi Is this arrayCGH? I am guessing from your array output that it was analyzed with UCSFSpot which is not the same as Spot (produced by CSIRO). You may find some functions in the package "aCGH". Alternatively, you can use the function read.marrayRaw and specified the columns you considered red/gr ...
written 12.8 years ago by Jean Yee Hwa Yang920
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Answer: A: issue in arrayQuality package
... Hi Longsi, Sorry ... there was also an update in arrayQuality. You need arrayQuality 1.0.8 which can be downloaded on http://www.bioconductor.org/repository/devel/package/html/arrayQuality .html Cheers YH On Wed, 29 Dec 2004, Longsi Ran wrote: > Hi, > > I am using R 2.0.1 with Biocond ...
written 12.9 years ago by Jean Yee Hwa Yang920
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Answer: A: issue in arrayQuality package
... Hi Longsi, There is a bug in the marray package. The path problem should be fixed in marray version 1.5.27 which you can download from http://www.bioconductor.org/repository/devel/package/html/marray.html Jean On Wed, 29 Dec 2004, Longsi Ran wrote: > Hi, > > I am using R 2.0.1 with Bi ...
written 12.9 years ago by Jean Yee Hwa Yang920
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layout for maQualityPlots
... Hi, Try the following: tmp <- layout(matrix(c(16, 1, 2, 2, 16, 0, 3, 3, 16, 4, 6, 6, 16, 5, 7, 7, 16, 8, 10, 11, 16, 9, 10, 11, 16, 12, 14, 14, 16, 13, 15,15), 4, 8), height = c(1, 10, 5, 5), width = c(11, 2, 5, 1.5, 5, 1.5, 5, 1.5)) layout.show(tmp) I thin ...
lung written 13.0 years ago by Jean Yee Hwa Yang920
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Answer: A: error in Loess normalization
... Hi, The new version of marray have included some sampling procedure to speed up the global loess code. I can test out your problem if you placed the .RData somewhere I can download. Cheers Jean > I am doing a loess normalization using a subset of genes that don’t change. > I get the follo ...
written 13.0 years ago by Jean Yee Hwa Yang920
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Answer: A: a problem with beginning
... Hi Shizhu, I will look into what is happening with the "browse" button. But a quick fix for the moment is to type "cn.target", "cn.layout" and "cn.genes" in the corresponding places and click on build. You should be able to read the data set in. Could you let me know what image analysis software ...
written 13.1 years ago by Jean Yee Hwa Yang920
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Answer: A: incomplete final row of every block
... Hi Mark, If you were trying out median normalization, try maNorm(my.oe, norm="m") How many lines do you have in the layout file? In order for print-tip loess to work on your array, you will need to set up my.layout@maSub properly. This should be a logical vector of length 7056. For the correspon ...
written 13.1 years ago by Jean Yee Hwa Yang920
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Answer: A: marray bug?
... Hi Istvan, Thank you for pointing this out, I will put in patch within the next 2 days. Cheers Jean On Tue, 12 Oct 2004, Istvan Albert wrote: > Hello, > > we just went trough a very frustrating process > of identifying a bug in marray. The same script kept > failing on a differen ...
written 13.1 years ago by Jean Yee Hwa Yang920

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