User: colonppg

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colonppg10
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10
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United States
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8 months ago
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2 years, 6 months ago
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c*******@gmail.com

Posts by colonppg

<prev • 11 results • page 1 of 2 • next >
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error/warning message while doing kmTCGA survival plot
... anyone encountered the same message while using kmTCGA? Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale. Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale. Warning message: In . ...
survival rtcga kmtcga written 8 months ago by colonppg10 • updated 7 months ago by jpgsabino0
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Comment: C: eset annotation issues, plus generate heatmap with correct gene symbol as row la
... Thanks, James... I think I have found the work around: it seems this will has to be done for individual genes... mygene.probe <-read.table(file="myprobesets.txt", blabla) gs<-select(hgu133plus2.db, mygene.probe, c("SYMBOL", "ENTREZID")) gs<-gs[order(gs$PROBEID), ]  # this will take care ...
written 2.4 years ago by colonppg10
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eset annotation issues, plus generate heatmap with correct gene symbol as row label
... Folks: need some help here... why it is so error prone and hard to deal with eset? # read in .cel files, normalize it, then try to attach annotation  mydata<-ReadAffy() mydata.rma<-rma(mydata) allprobe<-row.names(exprs(mydata.rma)) all.gs <- select(hgu133plus2.db, allprobe, c("SYMB ...
annotation eset written 2.4 years ago by colonppg10 • updated 2.4 years ago by James W. MacDonald45k
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paCalls(affyobject, "DABG/PSDABG") output dimension
... Dear all: I am really sorry for asking questions while at the same time has not been contributing to addressing people's issues. But here yet another issue while I am using the oligo package dabg<-paCalls(affyobject, method="DABG") dabgps <- paCalls(affyobject, method="PSDABG") I wonder i ...
oligo pacalls written 2.5 years ago by colonppg10 • updated 2.5 years ago by James W. MacDonald45k
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Comment: C: hugene10sttranscriptcluster.db missing some genes?
... hi, James: thanks, that's explains it: mydata<-frma(affyobj, target="core") I think the "core" made a lot of genes missing... thanks for your explanation. great help...   ...
written 2.5 years ago by colonppg10
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Comment: C: hugene10sttranscriptcluster.db missing some genes?
... Dear James: Thanks for your response, I do not think the warning will be an issue, but apparently this package is buggy because it misses a lot genes -- I downloaded the annotation from Affy and processed them under unix, those genes are there... I wonder if anyone encountered such issue and has a ...
written 2.5 years ago by colonppg10
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hugene10sttranscriptcluster.db missing some genes?
... Dear all: I have a project on hugene st 1.0 v1 I got all the probesets ID and give it to idsi, then try to get all entrezid and genesymbolls idsi<-probe.gs$PROBEID annot<-select(hugene10sttranscriptcluster.db, as.character(idsi), c("ENTREZID", "SYMBOL"), "PROBEID") Got error message: War ...
hugene10sttranscriptcluster.db annotation written 2.5 years ago by colonppg10 • updated 2.5 years ago by James W. MacDonald45k
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Comment: C: How do I use Limma to produce expression for each group, their P value and adjus
... hi, James: Thanks! this addressed my questions!  ...
written 2.5 years ago by colonppg10
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Answer: A: How do I use Limma to produce expression for each group, their P value and adjus
... Thanks, James... I think I still need to get deeper understanding of limma and how I should harness its power in the right way... so far I am impressed with its speed and convenience, I can see once I master it, it will make my life a lot easier... kudos to the builders of limma! But I have to argu ...
written 2.5 years ago by colonppg10
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Answer: A: How do I use Limma to produce expression for each group, their P value and adjus
... hi, Aaron: Thanks for your inputs, truly helpful... I tried to get coefficient by coef <- fit2.eBayes$coefficients Contrasts s.vs.ns c.vs.ns c.vs.s 1007_s_at -0.112430484 -0.025126351 0.087304133 1053_at 0.041222381 0.108865910 0.0676 ...
written 2.5 years ago by colonppg10

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