## User: colonppg

colonppg30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
2 years, 7 months ago
Joined:
4 years, 6 months ago
Email:
c*******@gmail.com

#### Posts by colonppg

<prev • 11 results • page 1 of 2 • next >
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... 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 . ...
written 2.6 years ago by colonppg30 • updated 2.6 years ago by jpgsabino10
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... 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$PROBEID), ] # this will take care ... written 4.4 years ago by colonppg30 1 answer 1.7k views 1 answer ... Folks: need some help here... why it is so error prone and hard to deal with eset? # read in .cel files, normalize it, then try to attach annotation mydata<-ReadAffy() mydata.rma<-rma(mydata) allprobe<-row.names(exprs(mydata.rma)) all.gs <- select(hgu133plus2.db, allprobe, c("SYMB ... written 4.4 years ago by colonppg30 • updated 4.4 years ago by James W. MacDonald51k 1 answer 691 views 1 answer ... Dear all: I am really sorry for asking questions while at the same time has not been contributing to addressing people's issues. But here yet another issue while I am using the oligo package dabg<-paCalls(affyobject, method="DABG") dabgps <- paCalls(affyobject, method="PSDABG") I wonder i ... written 4.5 years ago by colonppg30 • updated 4.5 years ago by James W. MacDonald51k 1 answer 608 views 1 answers ... hi, James: thanks, that's explains it: mydata<-frma(affyobj, target="core") I think the "core" made a lot of genes missing... thanks for your explanation. great help... ... written 4.5 years ago by colonppg30 1 answer 608 views 1 answers ... Dear James: Thanks for your response, I do not think the warning will be an issue, but apparently this package is buggy because it misses a lot genes -- I downloaded the annotation from Affy and processed them under unix, those genes are there... I wonder if anyone encountered such issue and has a ... written 4.5 years ago by colonppg30 1 answer 608 views 1 answer ... Dear all: I have a project on hugene st 1.0 v1 I got all the probesets ID and give it to idsi, then try to get all entrezid and genesymbolls idsi<-probe.gs$PROBEID annot<-select(hugene10sttranscriptcluster.db, as.character(idsi), c("ENTREZID", "SYMBOL"), "PROBEID") Got error message: War ...
written 4.5 years ago by colonppg30 • updated 4.5 years ago by James W. MacDonald51k
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... hi, James: Thanks! this addressed my questions!  ...
written 4.5 years ago by colonppg30
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... 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 4.5 years ago by colonppg30
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