[BioC] affy code archeology: expresso behavior for liwong/invariantset

[Martin Morgan]

On 01/24/2013 01:41 PM, David Eby [guest] wrote:
>
> Hello,
>
> I am in the midst of updating some inherited legacy code from R 2.8 and affy_1.20.2 to R 2.15.2 and affy_1.36.0, trying to fix some longstanding bugs.
>

That's a lot of water under the bridge (4 1/2 years? do you still have a working 
installation?)...

> Everything is going well except for some very different results coming out of an expresso call in one of my regression tests, specifically from:
> 	eset <- expresso(afbatch, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="pmonly",summary.method="liwong", verbose=TRUE)

...there is this at least in svn

affy$ svn log -r57229
------------------------------------------------------------------------
r57229 | jmacdon | 2011-08-04 12:18:56 -0700 (Thu, 04 Aug 2011) | 1 line

fixed bug in normalize.AffyBatch.invariantset
------------------------------------------------------------------------

and I've added Jim to the email for any insights.

Martin


> It's reporting expression values approx. 0.4-0.7x the values in the earlier setup (examples below).  I take for granted that many things have changed both at the R level and at the package level given the large leap in versions, but the difference seemed a bit odd since the results for other methods (RMA, GCRMA, MAS5) remained reasonably consistent in the update.
>
> It's quite possible that there is a package conflict or that I've accidentally broken something in the code base, though the legacy code itself is largely unchanged and the other regression tests seem to hold up pretty well.  I have looked at a number of things already, but before heading further down that path I wanted to check whether the implementation itself might have changed in a way where these differences would be expected.  Has there been a major change to liwong/invariantset somewhere along the way between 1.20.2 and 1.36.0?
>
> Checking with other members of the team, we're actually completely OK with the differences if they are in line with known changes to the affy package and can be explained to our users (this is a GenePattern module).
>
> Here is some example output for reference.  This is for a cut-down data set; I've seen similar results with 20 samples.  I can provide more if it would be helpful.
>>From the original setup (using write.table(exprs(eset)):
> "CL20030502207AA.CEL" "CL20030502208AA.CEL" "CL20030502307AA.CEL" "CL20030502308AA.CEL"
> "1007_s_at" 228.013212425507 214.877883873475 287.677963272274 306.997621485651
> "1053_at" 193.206766296132 168.017787218035 169.430151901596 157.819950438341
> <...snip...>
>
>>From the new setup:
> "CL20030502207AA.CEL" "CL20030502208AA.CEL" "CL20030502307AA.CEL" "CL20030502308AA.CEL"
> "1007_s_at" 500.169414439674 461.734001304198 704.700664579873 735.43106514776
> "1053_at" 321.921661422307 251.464504650157 261.491260842992 228.793486504634
> <...snip...>
>
> Thanks in advance!
> Regards,
> David
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793