User: Peter White

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Peter White70
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Posts by Peter White

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Possible bug with impute.knn
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080325/ b5894734/attachment.pl ...
written 9.7 years ago by Peter White70
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Comment: C: Limma, SAM and Fold Change Calculation
... Dear Holger and Gordon, Thanks a lot for your responses - that is very helpful. It is likely that both ways of calculating fold change are correct, but I agree with Gordon that it is most appropriate to report the fold change that was used to generate the significance statistic. I was also thinkin ...
written 10.4 years ago by Peter White70 • updated 7 months ago by Gordon Smyth32k
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Limma, SAM and Fold Change Calculation
... I wondered if anyone could comment on what is generally considered the most appropriate method of calculating fold change values from Affy data. I have a data set from a test vs. control experiment (n=3 in each group) performed on the MOE430_2 array. I used the Affy package to read in the CEL file d ...
affy limma gcrma siggenes written 10.4 years ago by Peter White70 • updated 7 months ago by Gordon Smyth32k
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Comment: C: Problem with ArrayQuality Package version 1.12
... Martin - I installed arrayQuality as you show below, but it did not install automatically with: source("http://www.bioconductor.org/getBioC.R") getBioC() and I am pretty sure it used to. Also, in the R GUI if you select the BioC repositories, then click Packages...Install Packages... arrayQuality ...
written 10.4 years ago by Peter White70
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Comment: C: Problem with ArrayQuality Package version 1.12
... Hi Agnes, That solution worked - I actually had to add the following functions to my code from version 1.10: gpFlagWt, setCtlCol, qpHexbin, qpImage, and qpS2N. Is there anyway to call these functions from the namespace file in the current version? Also, I noticed that arrayQuality is no longer in ...
written 10.4 years ago by Peter White70
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Comment: C: Problem with ArrayQuality Package version 1.12
... Dear Agnes, I was using your maQualityPlots code in my own function (see part of it below). The problem seems to be that in the newer version if I load the arrayQuality library I get an object not found error if I type gpFlagWt or setCtlCol. When I install the old version and type them in it return ...
written 10.4 years ago by Peter White70
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Problem with ArrayQuality Package version 1.12
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070706/ 9ad9dcd7/attachment.pl ...
written 10.4 years ago by Peter White70 • updated 10.4 years ago by Paquet, Agnes500

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Popular Question 9.7 years ago, created a question with more than 1,000 views. For Limma, SAM and Fold Change Calculation

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