User: Alvord, Greg DMS [Contr]

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Posts by Alvord, Greg DMS [Contr]

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Simple question on citation of an openVignette document
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written 12.4 years ago by Alvord, Greg DMS [Contr]160 • updated 12.4 years ago by Ben Bolstad1.2k
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Answer: A: PLMset and image function
... Hi Steve - I'm a newbie with Bioconductor and R. I am currently running R version 2.4.0 abnd BioConductor version 1.9, under Windows. I ran your commands on the Dilution data set and was able to get the image plot without any trouble. I did not receive any error indicating that the 'argument mus ...
written 12.7 years ago by Alvord, Greg DMS [Contr]160
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Proper references for CRAN and Bioconductor
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written 12.8 years ago by Alvord, Greg DMS [Contr]160 • updated 12.8 years ago by James W. MacDonald51k
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Answer: A: simpleaffy and yeast2cdf problems
... Hi Dan - This is the post I sent out only last week that may assist you with your problem. https://stat.ethz.ch/pipermail/bioconductor/2007-January/015514.html We ran into a similar problem with the soybeancdf environment. Hope this helps. Greg -----Original Message----- From: biocondu ...
written 12.9 years ago by Alvord, Greg DMS [Contr]160
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Modified qc.affy code for chip type: soybeancdf
... Hello All - Previously we experienced difficulty in obtaining quality control statistics from the library 'simpleaffy' for the soybean genome with chip type: soybeancdf. See our query of 9/14/06 to the list. After reading Crispin Miller's post to the list on 8/2/06 and following some useful sug ...
cancer cdf written 12.9 years ago by Alvord, Greg DMS [Contr]160
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Answer: A: RLE question for QC
... Enrique - We recently performed a series of elaborate quality control assessment procedures on probe level data for the soybean genome (24 CEL files under different strains and time conditions). Our RLE plots were nicely centered around zero, and the boxes (interquartile ranges) in the bo ...
written 13.0 years ago by Alvord, Greg DMS [Contr]160
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tasks of Background Correction and PM Correction in Preprocessing methods
... Mohammad - A possible start is to acquire the excellent Springer book (2005) entitled "Bioinformatics and Computational Biology Solutions Using R and Bioconductor" with editors Gentlemen, Carey, Huber, Irizarry, and Dudoit. Chapter 2, 'Preprocessing High-density Oligonucleotide Arrays' addr ...
preprocessing cancer written 13.0 years ago by Alvord, Greg DMS [Contr]160
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Answer: A: justPlier outputs negative values
... Hi Burak - I'm a newbie with Bioconductor and R, so I don't know whether this helps or hurts. I executed 'justPlier()' on several data sets on which I was somewhat familiar. I compared results with those I obtained using mas5 and rma. I am not qualified to say whether there are bugs in the justPl ...
written 13.1 years ago by Alvord, Greg DMS [Contr]160
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Problem obtaining QC statistics from 'simpleaffy'
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written 13.2 years ago by Alvord, Greg DMS [Contr]160 • updated 13.2 years ago by Jenny Drnevich2.2k
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Your FANTASTIC help with soybean
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written 13.4 years ago by Alvord, Greg DMS [Contr]160

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