Solved. Before finalize a release, would you mind making sure it
works on your end. Install aroma.affymetrix 2.13.0-9001 by running
the following in a fresh R session:
source('http://callr.org/install#HenrikBengtsson/aroma.affymetrix@2.13.0-9001')
Then retry with
This is odd for several reasons, e.g. I'm puzzled how you ended up with a
monocell CDF previously but now it gives an error. Let's troubleshoot
more...
What does troubleshoot() output directly after you get that error?
Henrik
On Jan 23, 2015 7:23 AM, Qingzhou Zhang zqznept...@gmail.com wrote:
On Jan 23, 2015 7:36 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote:
This is odd for several reasons, e.g. I'm puzzled how you ended up with a
monocell CDF previously but now it gives an error. Let's troubleshoot
more...
What does troubleshoot() output directly after you get that error?
I
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
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)
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
