[BioC] HTqPCR: new qPCRset objects problem
Heidi Dvinge
heidi at ebi.ac.uk
Tue Mar 8 14:14:51 CET 2011
Hi Wenbo,
thanks for the reproducible examples. Sorry for the delay in getting back
to you.
> 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]
>
This seems to be an issue with how the qPCRset object is created. I'll
work on a fix and commit it to the development repository.
In the meantime, it should work if you also add the "flag" slot. For example:
> 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))), flag = as.data.frame(array("OK",
c(n,n))))
> raw[,1]
An object of class "qPCRset"
Size: 48 features, 1 samples
Feature types:
Feature names: A1 A2 A3 ...
Feature classes:
Feature categories: OK
Sample names: S1 NA NA ...
> raw[1,]
An object of class "qPCRset"
Size: 1 features, 48 samples
Feature types:
Feature names: A1 NA NA ...
Feature classes:
Feature categories: OK
Sample names: S1 S2 S3 ...
If you add a data frame with flags, do your downstream errors with
filterCtData etc. persist?
Cheers
\Heidi
>> 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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