[BioC] NA instead of block row and ID and column values

[michael watson (IAH-C)]

Ankit

Can you please include some sample code so we can figure out exactly
what it is you are doing?

Many thanks
Mick

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Ankit Pal
Sent: 18 May 2005 10:12
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] NA instead of block row and ID and column values


Dear All,
Please ignore my previous query titled "The meaning of
NA in all the result summary".
I am reframing my question.
I am using a set of gpr files for analysis with the
LIMMA package.
On completion of the analysis, I get a set of 2000
genes with p value< 0.05.
There are some spots in this file which contain the M,
A, T, p and B values but in the fields named Block row
column and ID there is an "NA". (See attachment)
The block, row, column and ID values are inherited
from the GPR files and are present in the same. So why
did LIMMA replace them with a "NA"?
In the total set of 30010 genes, 7270 have NA's in
them, which is not the case in the corresponding gpr
file.
Is this because the NA represents spots that did not
get through the spot filtering step?
Looking forward to a reply,
thank you,
-Ankit