[BioC] HTqPCR: new qPCRset objects problem
Heidi Dvinge
heidi at ebi.ac.uk
Wed Mar 2 23:33:31 CET 2011
Hi Wenbo,
> Dear List,
>
> When trying to use HTqPCR to analyze data under R 2.12, my code which
> works under R 2.10 doesn't work any more.
>
> When I'm using function filterCtData, I got some Warning messages. If
> I ignore the warnings, a error will happen when using filterCtData
> function.
> I concluded some error happened at q[!index,], so I check the source
> code and do some small experiments. I substitute q <- q[!index, ] by
> featureCategory(q) <- featureCategory
> (q)[!index,], and then no error happens.
>
>> q.norm <- normalizeCtData(sr.norm,norm="quantile")
>
> Warning messages:
> 1: In `[<-.factor`(`*tmp*`, ri, value = "normalizeCtData(q = sr.norm,
> norm = \"quantile\")") :
> invalid factor level, NAs generated
> 2: In `[<-.factor`(`*tmp*`, ri, value = "normalizeCtData(q = sr.norm,
> norm = \"quantile\")") :
> invalid factor level, NAs generated
>
as far as I remember, there were some bugs introduced with subsetting when
I added rbind and cbind methods for qPCRset objects to HTqPCR (oops).
These should hopefully have been fixed in the development version, 1.5.3.
Would it be possible for you to install the development version and see if
these errors still occur? Although it generally isn't recommendable to run
devel versions of packages on the release version of R/Bioconductor, I've
tried so with HTqPCR before without problems. Just download whatever
version fits your OS from
http://www.bioconductor.org/packages/devel/bioc/html/HTqPCR.html, and
install it manually in R.
If installing the devel version isn't feasible for you, or if these errors
still occur, then please report back here and I'll see what I can do about
it.
Best
\Heidi
>> q.Filt <- filterCtData( q.norm, remove.category="Undetermined",
>> n.category = 36, remove.name=c(HK.miR.rm,"MammU6"))
> Error in names(x) <- value :
> 'names' attribute [41] must be the same length as the vector [0]
>
>> traceback()
> 6: `colnames<-`(`*tmp*`, value = c("C1", "C2", "C3", "C4", "C5",
> "C6", "C7", "S1", "S2", "S3", "S4", "S5", "S6", "S7", "T1", "T10",
> "T11", "T12", "T13", "T2", "T3", "T4", "T5", "T6", "T7", "T8",
> "T9", "U1", "U.1", "U10", "U12", "U13", "U2", "U.2", "U3", "U.3",
> "U4", "U5", "U6", "U8", "U9"))
> 5: flag(x)
> 4: .local(x, i, j, ..., drop)
> 3: q[!index, ]
> 2: q[!index, ]
> 1: filterCtData(q.norm, remove.category = "Unreliable",
> n.category = 36, remove.name = c(HK.miR.rm, "MammU6"))
>
>
> I thought the subsetting problem may come from some mistakes at earlier
> step.
> I find if use the qPCRset test object, we can subset the object by
> specific number such as qPCRraw[,1] or qPCRraw[1,]. But if we create a
> qPCRset object by new function, the subsetting doesn't works. I try
> the follow code under i386-pc-mingw32 Windows with R version 2.10.1
> and HTqPCR version 1.0.0, under x86_64-unknown-linux-gnu with R
> version 2.11.1 and HTqPCR version 1.2.0 and under x86_64-pc-linux-gnu
> (64-bit) with R version 2.12.2 and HTqPCR version 1.4.0.
>
>> n<- 48
>> temp<- matrix(rnorm(n*n),ncol=n,nrow=n)
>> raw <- new("qPCRset", exprs=temp, sampleNames=paste("S", 1:n, sep=""),
>> featureNames=paste("A", 1:n, sep=""),
>> featureCategory=as.data.frame(array("OK", c(n,n))))
>
>> raw[,1]
> Error in names(x) <- value :
> 'names' attribute [1] must be the same length as the vector [0]
>> raw[1,]
> Error in names(x) <- value :
> 'names' attribute [48] must be the same length as the vector [0]
>
> Row subsetting and column subsetting error both happens at R 2.11.1
> and R 2.12.2. But only column subsetting error happens at R 2.10.1. I
> think that's the reason why my old code doesn't work with new version
> R and HTqPCR. I would really appreciate any suggestions that could
> help me solve this problem.
>
> Windows with R 2.10.1 sessionInfo:
> R version 2.10.1 (2009-12-14)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] HTqPCR_1.0.0 limma_3.2.3 RColorBrewer_1.0-2 Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] affy_1.24.2 affyio_1.14.0 gdata_2.7.1
> [4] gplots_2.7.4 gtools_2.6.1 preprocessCore_1.8.0
> [7] tools_2.10.1
>
> Linux with R 2.11.1 sessionInfo:
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C
> [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591
> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso88591
> [7] LC_PAPER=en_US.iso88591 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] HTqPCR_1.2.0 limma_3.4.5 Biobase_2.8.0 SLqPCR_1.14.0
> [5] RColorBrewer_1.0-2
>
> loaded via a namespace (and not attached):
> [1] affy_1.26.1 affyio_1.16.0 gdata_2.8.1
> [4] gplots_2.8.0 gtools_2.6.2 preprocessCore_1.10.0
> [7] tools_2.11.1
>
> Linux with R 2.12.2 sessionInfo:
> R version 2.12.2 (2011-02-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=en_US.utf8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] HTqPCR_1.4.0 limma_3.6.9 RColorBrewer_1.0-2
> Biobase_2.10.0
> [5] SLqPCR_1.16.0
>
> loaded via a namespace (and not attached):
> [1] affy_1.28.0 affyio_1.18.0 gdata_2.8.1
> [4] gplots_2.8.0 gtools_2.6.2 preprocessCore_1.12.0
> [7] tools_2.12.2
>
> Best,
> Wenbo Mu
>
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