Hi Henrik,
I was processing HG-U133_Plus_2 datasets. While extracting probeset
summaries(chip effects) as a data frame, I only got 27604 objs * n
variables.
I was hoping to get a data frame of 54675 objs., which equals the number of
units in HG-U133_Plus_2 chip. Am I missing some steps, or
Hi,
Please check old discussions. I remember there were discussions. I had the
same issue.
Most probably, you did not install if you were using Linux system
On Wednesday, January 21, 2015 at 3:46:49 PM UTC+2, Juanjo Lozano wrote:
Hi,
I found
Error: Package not loaded: sfit
Execution
Hi,
I have tried this and works good but at the end I need the information
whether there is a gain or loss at the segment. I will use GLAD model to
get gain or loss at a segment. My samples and controls are completely
unrelated so I am little bit doubtful whether I am doing right or not.
Thanks. I can *not* reproduce this, e.g.
ces
ChipEffectSet:
Name: GSE9890
Tags: GRBC,QN,RMA,oligo
Path: plmData/GSE9890,GRBC,QN,RMA,oligo/HG-U133_Plus_2
Platform: Affymetrix
Chip type: HG-U133_Plus_2,monocell
Number of arrays: 10
Names: GSM249671, GSM249672, GSM249673, ..., GSM249680 [10]
Time
Hi, Henrik,
Thanks for the reply!
Here is my code:
library(aroma.affymetrix)
RawName = Project1
RawChipType = HG-U133_Plus_2
ces - doGCRMA(RawName, chipType = RawChipType)
data - extractDataFrame(ces, units = NULL, addNames = TRUE)
Here is the sessionInfo()
R version 3.1.1 (2014-07-10)
Hi guys,
here are some late feedback on this discussion:
* When talking about copy numbers, it is important to always be very
clear and distinguish between whether we talk about normal/germline
CNs or tumor CNs. The former take integer CN levels (0, 1, 2, 3,
...), whereas for tumors we very
On Thu, Jan 22, 2015 at 5:44 AM, Qingzhou Zhang zqznept...@gmail.com wrote:
Hi Henrik,
I was processing HG-U133_Plus_2 datasets. While extracting probeset
summaries(chip effects) as a data frame, I only got 27604 objs * n
variables.
I was hoping to get a data frame of 54675 objs., which
