[BioC] HTqPCR: new qPCRset objects problem
Wenbo Mu
muwenbo.prc at gmail.com
Thu Mar 3 01:02:30 CET 2011
Hi, Heidi,
Thank your for your help.
I installed the HTqPCR development version, 1.5.3 and got warnings.
But when check the session info, it seems correctly installed.
Warning message:
In install.packages(c("HTqPCR", "../HTqPCR_1.5.3.tar.gz"), :
installation of package 'HTqPCR' had non-zero exit status
Then I test the subsetting in the same way, it seems still not work.
> 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]
> 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_1.5.3 limma_3.6.9 RColorBrewer_1.0-2 Biobase_2.10.0
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
Wenbo Mu
On Wed, Mar 2, 2011 at 4:33 PM, Heidi Dvinge <heidi at ebi.ac.uk> wrote:
> 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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>
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