[BioC] limma - background correct method=none

[Helen Cattan]

I have checked that the gpr files are correct and the column headings
are fine and they are. I've done the same without the flagging and get
(not very) different results so does this mean I can assume my flagging
is working ok? Is there a way for me to check the data is read and
flagged correctly? - to look at part of the RG list and the flagged
values?
Also I have no missing values in either foreground or background on the
gpr files in my other post so suspect there is a peculiarity in the
reading somewhere.

Thanks,
Helen

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Matthew
Hannah
Sent: 19 April 2004 11:00
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] limma - background correct method=none


The first code and top table is with default subtract (with the file
with
0's for BG, and the second top table is that obtained using 
RG=backgroundCorrect(RG, method="none") on the original data.

The obvious is to double check that the .gpr files are correct, and that

you haven't mixed medians and means by mistake when replacing BG with
the 0's.
A problem with these files may also explain the high NA's and missing
values 
in your other post. I'm not sure on the file format, but check the
column 
headings correspond to the correct columns. I once had such a column
shift 
when writing spot output to .txt files with all sorts of 'interesting'
results.

The other suggestion/question is could the wt.fun=wtflags(0), be having
any effect?
Try the same without this, but I'd definetely look at the source data
first.

HTH,
Matt

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