[BioC] HTqPCR: new qPCRset objects problem
Heidi Dvinge
heidi at ebi.ac.uk
Thu Mar 10 16:32:14 CET 2011
Hi Wenbo,
> Hi, Heidi,
>
> Thank for your reply. After adding the "flag" slot, I met no error in
> downstream analysis, but only some warnings like the following. I
> think it doesn't affect the performance of the function.
> I run the code of normalizeCtData line by line, and found the warning
> happens at the last command "q at history <- rbind(q at history,
> capture.output(match.call(normalizeCtData)))". The similar warning
> also happens when running other functions like filterCtData. I'm not
> sure whether it's the problem of option setting of my R environment or
> of the function. I hope this information could be helpful to improve
> this great package.
>
> Warning messages:
> 1: In `[<-.factor`(`*tmp*`, ri, value = "normalizeCtData(q = raw.cat,
> norm = \"deltaCt\", deltaCt.genes = HK.miR.rm)") :
> invalid factor level, NAs generated
> 2: In `[<-.factor`(`*tmp*`, ri, value = "normalizeCtData(q = raw.cat,
> norm = \"deltaCt\", deltaCt.genes = HK.miR.rm)") :
> invalid factor level, NAs generated
>
thanks for the detailed feedback. I think I've fixed the functions that
caused the first error, but need to do some more testing to ensure that it
doesn't cause any problems downstream.
While doing that I'll also check what causes the problems with the history
slot. You're right that this doesn't affect the performance of the
functions though. I doubt it's related to the settings of your R session,
it's more likely a question of how I initialize some objects.
Cheers
\Heidi
> Thanks again,
>
> Wenbo Mu
>
>
>
>
> On Tue, Mar 8, 2011 at 7:14 AM, Heidi Dvinge <heidi at ebi.ac.uk> wrote:
>> 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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