User: colonppg

gravatar for colonppg
colonppg10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
1 month ago
Joined:
1 year, 11 months ago
Email:
c*******@gmail.com

Posts by colonppg

<prev • 11 results • page 1 of 2 • next >
0
votes
1
answer
92
views
1
answer
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 4 weeks ago by colonppg10 • updated 4 days ago by jpgsabino0
0
votes
1
answers
611
views
1
answers
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 22 months ago by colonppg10
2
votes
1
answer
611
views
1
answer
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 22 months ago by colonppg10 • updated 22 months ago by James W. MacDonald43k
0
votes
1
answer
318
views
1
answer
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 23 months ago by colonppg10 • updated 23 months ago by James W. MacDonald43k
0
votes
1
answers
215
views
1
answers
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 23 months ago by colonppg10
0
votes
1
answers
215
views
1
answers
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 23 months ago by colonppg10
0
votes
1
answer
215
views
1
answer
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 23 months ago by colonppg10 • updated 23 months ago by James W. MacDonald43k
0
votes
5
answers
1.1k
views
5
answers
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 23 months ago by colonppg10
0
votes
5
answers
1.1k
views
5
answers
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 23 months ago by colonppg10
0
votes
5
answers
1.1k
views
5
answers
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 23 months ago by colonppg10

Latest awards to colonppg


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 133 users visited in the last hour