Ryan,
I've made these changes to the frmaTools package (should show up in version
1.21.1):
Old:
if(!identical(as.character(pmi),rownames(pms))) stop("Mismatch between
pmindex and rownames of pms")
Nes:
if(!identical(sprintf("%i",pmi),rownames(pms))) stop("Mismatch between
pmindex and rownames
Actually, the code looks like it should be adding these names, so I need to
go back through my code and get back to you on that issue.
On Jul 7, 2015 9:58 AM, "Ryan C. Thompson" wrote:
> I've also encoundered another problem, this time I believe related to a
> change the the frma package which re
I've also encoundered another problem, this time I believe related to a
change the the frma package which requires a corresponding change in the
frmaTools package. Apparently frma has added a check for equality of
probe names in various places, and frmaTools does not store these names,
which me
Ryan,
Thanks for pointing these out. I'll look into them soon, but I imagine your
assessment is correct.
Best,
Matt
On Mon, Jul 6, 2015 at 5:42 PM, Ryan C. Thompson
wrote:
> I also discovered another apparent bug later in the same function. The
> second to last line of makeVectorsAffyBatch i
I also discovered another apparent bug later in the same function. The
second to last line of makeVectorsAffyBatch is
vers <- ifelse(!is.null(cdfname),
as.character(packageVersion(cdfname)), "")
If cdfname is NULL, this line will throw an error because the second
argument to ifelse will
Hello,
I just encountered a bug in frmaTools that makes it impossible to use on
certain array platforms. The following lines in makeVectorsAffyBatch
fail on an AffyBatch object on the hthgu133pluspm platform:
pms <- pm(object)
pns <- probeNames(object)
pmi <- unlist(pmindex(object
