User: Jia, Li NIH/NCI [C]

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4 years, 11 months ago
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5 years, 10 months ago
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Posts by Jia, Li NIH/NCI [C]

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Comment: C: create the expression set
... Thanks Jim for the reply! I don't proceed to lmFit on limma, I only need to generate ExpressionSet and use it for the SOM. Thanks, Li On 6/26/14 2:51 PM, "James W. MacDonald" wrote: >You don't need an ExpressionSet to analyze data using limma. You can >instead use a matrix. See ?lmFit for ...
written 5.0 years ago by Jia, Li NIH/NCI [C]70
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Comment: C: error on detecting regions
... Hi Pan, It still has the error message after the update. There are total 80 samples, but I only picked subgroup 42 samples to compare as mentioned in the first email. > ResultStage <- detectDMR.slideWin(Mset, sampleType=c(postAcute, pre)) Smoothing Chromosome chr1 ... Smoothing Chromosome ch ...
written 5.0 years ago by Jia, Li NIH/NCI [C]70
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Comment: C: error on loading ratioConvert() in minfi
... Hi Kasper, You are right, I restarted the new session, it works. But when I tried to move along the analysis to generate the GenomeratioSet, it has another error message: > gRatioSet <- mapToGenome(ratioSet, mergeManifest = TRUE) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE ...
written 5.1 years ago by Jia, Li NIH/NCI [C]70
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Comment: C: error on loading ratioConvert() in minfi
... Hi Kasper, We just upgraded to version 1.10.0, but it still doesn't work. > library(minfi) > ratioSet <- ratioConvert(MSet.swan, what = c("beta", "M", "both"), keepCN = TRUE) Error: could not find function "ratioConvert" Thanks, Li From: Kasper Daniel Hansen > Date: Wed, 21 May 2014 ...
written 5.1 years ago by Jia, Li NIH/NCI [C]70
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Comment: C: org.Hs.eg.db package loading issues
... Thanks Dan! It works. Li On 7/26/13 1:43 PM, "Dan Tenenbaum" wrote: >On Fri, Jul 26, 2013 at 8:41 AM, Guest [guest] >wrote: >> >> Hi, >> >> When I run the R code on analysis of HuGene2.0ST array, it generated an >>error as follows: >> >>> source ...
written 5.9 years ago by Jia, Li NIH/NCI [C]70
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Comment: C: org.Hs.eg.db package loading issues
... Thanks Ekta! I just got message from Dan who suggested to update to 3.0.1, which works. Have a nice weekend! Li From: Ekta Jain > Date: Fri, 26 Jul 2013 21:16:48 +0530 To: "Guest [guest]" > Cc: >, Mac User > Subject: Re: [BioC] org.Hs.eg.db package loading issues Hi, I got some error t ...
written 5.9 years ago by Jia, Li NIH/NCI [C]70
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Comment: C: oligo package attaching phenodata for HuGene2.0 ST array
... Hi Jim, Thanks for the prompt reply. When I tested on the first command you sent to us, it generated an error. > x <- varMetadata(pd) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ?varMetadata? for signature ?"data.frame"? Please advise ag ...
written 5.9 years ago by Jia, Li NIH/NCI [C]70

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