One other quick question, does anyone know a way I could sort the data
in column the HuEx1_0028 or HuEx1_0035
by descending order?
*#result* *(how do i go about changing this unitName and
groupName)*
unitName groupName unit group cellHuEx1_0028 HuEx1_0035
1 2315373 23153741 1
Thanks for the quick response Mark,
Would you mind showing me an example of the code required to connect
the data with the csv? I'm still pretty new to coding as well
So to use exonmap would I would still need to connect the unit name
with the csv before utilizing the data correct?
Thanks,
-Kripa
Hi Yu Chuan.
As I mentioned before, I was unable to reproduce your error from a
test dataset on my system. Its hard to know the history of your
environment, so what I suggest you do is start from a brand new
session, and run the commands start to finish. There are a couple
ways to do thi
Hi Elizabeth,
Thanks for your comments. They are very helpful!
Best,
Yu Chuan
On Dec 1, 9:39 am, Elizabeth Purdom wrote:
> > Also, what does it mean if the boxplot for a chip's exon-level NUSE
> > suggests that this chip maybe an outlier (i.e. the median is higher
> > than those of other chips)
Mark,
I pulled out some chip effectsthe NUSE are still all 0s.
> cesTr <- getChipEffectSet(plmTr)
>
> trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
> dim(trFit)
[1] 3 13
> trFit
unitName groupName unit group cell 20091119_Colon4_Exon2
1 2315251 23152521 11
> Also, what does it mean if the boxplot for a chip's exon-level NUSE
> suggests that this chip maybe an outlier (i.e. the median is higher
> than those of other chips), while its RLE boxplot doesn't suggest that
> (its RLE boxplot align with others)? Should I treat this chip as an
> outlier at a
Hi Yu Chuan.
I'm still mystified by this. Can you check that the PLM was
successfully fit? Pull out some chip effects, maybe.
Cheers,
Mark
On 25-Nov-09, at 4:51 AM, Yu Chuan wrote:
> Mark,
>
> I think the below info. may help too. Looks like all the gene-level
> NUSE are 0. How could this h
Mark,
I think the below info. may help too. Looks like all the gene-level
NUSE are 0. How could this happen?
z <- plotNuse(qamTr)
> z
$`20091119_Colon4_Exon2`
$`20091119_Colon4_Exon2`$stats
[1] 0 0 0 0 0
$`20091119_Colon4_Exon2`$n
[1] 18705
$`20091119_Colon4_Exon2`$conf
[1] 0 0
$`20091119_Col
Hi Mark,
Thanks for your prompt reply. Below is my complete R code together
with error information. I tried what you suggested, but the resulted
NUSE plot still looks the same.
Also, what does it mean if the boxplot for a chip's exon-level NUSE
suggests that this chip maybe an outlier (i.e. the me
Hi Mark,
Yes, I did forget that line. I just tried it and it works!
Thanks so much for your help,
Enid
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInf
Hi Enid.
My apologies. Looks like I forgot a line in my script, a line that
you must have forgotten in your original script. You'll need to fit()
the plm before calculating residuals ...
You'll want something like:
[...]
plm <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plm, verbose=verbose)
rs
Hi Mark,
Thanks for your reply. I tried the codes you posted, but had the same
problem.
library(aroma.affymetrix)
verbose <- Arguments$getVerbose(-20, timestamp=TRUE)
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType,
tags="coreR3,A20071112,EP")
cs <- AffymetrixCelSet$by
Hi Enid.
I was unsuccessful in repeating your problem. I ran the script below
from a fresh session on the Affy tissues dataset using
aroma.affymetrix 1.2.0 ... and I get results. I don't think I've run
FIRMA on as few as 4 samples as your example suggests, but in theory
that shouldn't b
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