Hi Yu Chuan.
Comments below.
On 24-Nov-09, at 1:00 PM, Yu Chuan wrote:
Hi,
I am pre-processing 8 exon arrays (Hu-Ex-1_0-st-v2) and doing quality
assessment. When I plotted the NUSE using plotNUSE, I found that the
y-
axis limit is too wide, such that the boxplots were all squeezed
Hi Jiang.
A couple quick comments below.
On 20-Nov-09, at 10:07 AM, camelbbs wrote:
Hi,
After I got the firma scores, how can i analyze it. I see boxplot of
firma scores in the paper. So how i can get the same result.
You can use the boxplot() command on your matrix of FIRMA scores?
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
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
