Hi,
I am trying to plot different graphs using cummerRbund for bacterial
transcriptome.
I get all the plots except the volcano plot.
I am using : tophat-1.3.3.Linux_x86_64, samtools-0.1.12a,
cufflinks-1.2.0.Linux_x86_64
I get following error:
library("cummeRbund")
cuff = readCufflinks()
cuff
gene = genes(cuff)
v = csVolcano(gene)
v
Error in grid.pretty(range) :
infinite axis extents [GEPretty(-1.79769e+308,1.79769e+308,5)]
Can someone please explain where am i going wrong?
R session info is given below:
sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] cummeRbund_1.0.0 ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4
[5] plyr_1.6 RSQLite_0.10.0 DBI_0.2-5
--
Regards,
Chintan Vora
Sr. Research Associate
Xcelris Labs Ltd.
Old Premchandnagar Road,
Bodakdev, Ahmedabad-380 054 India.
Tel: +91-79-66197777/66311114
Fax: +91-79-66309341
Email: chintan.vora@xcelrislabs.com
Website: www.xcelrisgenomics.com
"Please don't print this e-mail unless you really need to. Save Paper,
Save Trees"
----------------------------------------------------------------------
----------
Disclaimer\ \ \ Any views or opinions presented in
this...{{dropped:13}}
Hi,
I'm cc'ing Loyal (package maintainer) in case he didn't see this
message.
Valerie
On 11/30/2011 11:03 PM, Chintan Vora - Xcelris wrote:
> Hi,
>
> I am trying to plot different graphs using cummerRbund for bacterial
> transcriptome.
> I get all the plots except the volcano plot.
>
> I am using : tophat-1.3.3.Linux_x86_64, samtools-0.1.12a,
> cufflinks-1.2.0.Linux_x86_64
>
> I get following error:
>
> library("cummeRbund")
> cuff = readCufflinks()
> cuff
> gene = genes(cuff)
> v = csVolcano(gene)
> v
> Error in grid.pretty(range) :
> infinite axis extents [GEPretty(-1.79769e+308,1.79769e+308,5)]
>
> Can someone please explain where am i going wrong?
>
> R session info is given below:
>
> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid stats graphics grDevices utils datasets
methods
> [8] base
>
> other attached packages:
> [1] cummeRbund_1.0.0 ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4
> [5] plyr_1.6 RSQLite_0.10.0 DBI_0.2-5
>
Hi,
(Thank you for forwarding this to me Valerie, I did in fact miss.)
You must provide two additional arguments to csVolcano. You need to
specify which two sample for which you would like to plot the log fold
change, since this is a pairwise comparison plot.
Please try something like the following:
cuff<-readCufflinks()
gene <- genes(cuff)
v<-csVolcano(gene, "sampleA", "sampleB")
v
I hope this helps.
Cheers,
Loyal
On Dec 2, 2011, at 11:46 AM, Valerie Obenchain wrote:
> Hi,
>
> I'm cc'ing Loyal (package maintainer) in case he didn't see this
message.
>
> Valerie
>
>
> On 11/30/2011 11:03 PM, Chintan Vora - Xcelris wrote:
>> Hi,
>>
>> I am trying to plot different graphs using cummerRbund for
bacterial
>> transcriptome.
>> I get all the plots except the volcano plot.
>>
>> I am using : tophat-1.3.3.Linux_x86_64, samtools-0.1.12a,
>> cufflinks-1.2.0.Linux_x86_64
>>
>> I get following error:
>>
>> library("cummeRbund")
>> cuff = readCufflinks()
>> cuff
>> gene = genes(cuff)
>> v = csVolcano(gene)
>> v
>> Error in grid.pretty(range) :
>> infinite axis extents [GEPretty(-1.79769e+308,1.79769e+308,5)]
>>
>> Can someone please explain where am i going wrong?
>>
>> R session info is given below:
>>
>> sessionInfo()
>> R version 2.14.0 (2011-10-31)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=C LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] grid stats graphics grDevices utils datasets
methods
>> [8] base
>>
>> other attached packages:
>> [1] cummeRbund_1.0.0 ggplot2_0.8.9 proto_0.3-9.2
reshape_0.8.4
>> [5] plyr_1.6 RSQLite_0.10.0 DBI_0.2-5
>>
>
My final report text file reads in fine. Then things get ugly. Any
suggestions,
casual or otherwise, appreciated!
Tom
data <- lumiR("FinalReport.txt", lib.mapping = "lumiHumanIDMapping")
> data
ExpressionSet (storageMode: lockedEnvironment)
assayData: 47231 features, 12 samples
element names: detection, exprs
protocolData: none
phenoData
sampleNames: 6303230026_A 6303230026_B ... 6303230026_L (12 total)
varLabels: sampleID
varMetadata: labelDescription
featureData
featureNames: Ku8QhfS0n_hIOABXuE fqPEquJRRlSVSfL.8A ...
N8t5EuJCr0Tk9.zHno (47231 total)
fvarLabels: ProbeID TargetID ... DEFINITION (9 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: lumiHumanAll.db
Data normalization seems not to work. Maybe the final report text
files is already normalized..
Next, I want to know what these nuids are, but that goes very poorly.
getSYMBOL(rownames(exprs(data)), lumiHumanAll.db)
Error in mget(x, envir = getAnnMap(what, chip = data, load = load),
ifnotfound = NA) :
error in evaluating the argument 'envir' in selecting a method for
function 'mget'
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.6.9 lumiHumanAll.db_1.12.0
org.Hs.eg.db_2.4.6
[4] annotate_1.28.0 lumiHumanIDMapping_1.8.0 RSQLite_0.9-4
[7] DBI_0.2-5 AnnotationDbi_1.12.0 lumi_2.2.1
[10] Biobase_2.10.0
loaded via a namespace (and not attached):
[1] affy_1.28.0 affyio_1.18.0 grid_2.12.0
[4] hdrcde_2.15 KernSmooth_2.23-6 lattice_0.19-33
[7] MASS_7.3-11 Matrix_0.999375-50 methylumi_1.6.1
[10] mgcv_1.7-6 nlme_3.1-98 preprocessCore_1.12.0
[13] tools_2.12.0 xtable_1.5-6
[[alternative HTML version deleted]]
On 12/02/2011 01:38 PM, Thomas H. Hampton wrote:
> My final report text file reads in fine. Then things get ugly. Any
suggestions,
> casual or otherwise, appreciated!
>
> Tom
>
> data<- lumiR("FinalReport.txt", lib.mapping = "lumiHumanIDMapping")
>
>
>> data
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 47231 features, 12 samples
> element names: detection, exprs
> protocolData: none
> phenoData
> sampleNames: 6303230026_A 6303230026_B ... 6303230026_L (12
total)
> varLabels: sampleID
> varMetadata: labelDescription
> featureData
> featureNames: Ku8QhfS0n_hIOABXuE fqPEquJRRlSVSfL.8A ...
> N8t5EuJCr0Tk9.zHno (47231 total)
> fvarLabels: ProbeID TargetID ... DEFINITION (9 total)
> fvarMetadata: labelDescription
> experimentData: use 'experimentData(object)'
> Annotation: lumiHumanAll.db
>
>
> Data normalization seems not to work. Maybe the final report text
files is already normalized..
>
> Next, I want to know what these nuids are, but that goes very
poorly.
>
> getSYMBOL(rownames(exprs(data)), lumiHumanAll.db)
> Error in mget(x, envir = getAnnMap(what, chip = data, load = load),
ifnotfound = NA)
> error in evaluating the argument 'envir' in selecting a method
for function 'mget'
Hi Tim -- I think you're just wanting to supply the annotation db as a
character string rather than symbol
getSYMBOL(featureNames(data), annotation(data))
Martin
>
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] limma_3.6.9 lumiHumanAll.db_1.12.0
org.Hs.eg.db_2.4.6
> [4] annotate_1.28.0 lumiHumanIDMapping_1.8.0
RSQLite_0.9-4
> [7] DBI_0.2-5 AnnotationDbi_1.12.0 lumi_2.2.1
> [10] Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] affy_1.28.0 affyio_1.18.0 grid_2.12.0
> [4] hdrcde_2.15 KernSmooth_2.23-6 lattice_0.19-33
> [7] MASS_7.3-11 Matrix_0.999375-50 methylumi_1.6.1
> [10] mgcv_1.7-6 nlme_3.1-98
preprocessCore_1.12.0
> [13] tools_2.12.0 xtable_1.5-6
>
>
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
Hi,
Thank you for response.
Its working.
I thought that it should work without passing the sample names.
Regards,
Chintan Vora
Sr. Research Associate
Xcelris Labs Ltd.
Old Premchandnagar Road,
Bodakdev, Ahmedabad-380 054 India.
Tel: +91-79-66197777/66311114
Fax: +91-79-66309341
Email: chintan.vora@xcelrislabs.com
Website: www.xcelrisgenomics.com
On 12/02/2011 11:41 PM, Loyal Goff wrote:
> Hi,
> (Thank you for forwarding this to me Valerie, I did in fact miss.)
>
> You must provide two additional arguments to csVolcano. You need to
specify which two sample for which you would like to plot the log fold
change, since this is a pairwise comparison plot.
>
> Please try something like the following:
>
> cuff<-readCufflinks()
> gene<- genes(cuff)
> v<-csVolcano(gene, "sampleA", "sampleB")
> v
>
>
> I hope this helps.
>
> Cheers,
> Loyal
>
>
> On Dec 2, 2011, at 11:46 AM, Valerie Obenchain wrote:
>
>> Hi,
>>
>> I'm cc'ing Loyal (package maintainer) in case he didn't see this
message.
>>
>> Valerie
>>
>>
>> On 11/30/2011 11:03 PM, Chintan Vora - Xcelris wrote:
>>> Hi,
>>>
>>> I am trying to plot different graphs using cummerRbund for
bacterial
>>> transcriptome.
>>> I get all the plots except the volcano plot.
>>>
>>> I am using : tophat-1.3.3.Linux_x86_64, samtools-0.1.12a,
>>> cufflinks-1.2.0.Linux_x86_64
>>>
>>> I get following error:
>>>
>>> library("cummeRbund")
>>> cuff = readCufflinks()
>>> cuff
>>> gene = genes(cuff)
>>> v = csVolcano(gene)
>>> v
>>> Error in grid.pretty(range) :
>>> infinite axis extents [GEPretty(-1.79769e+308,1.79769e+308,5)]
>>>
>>> Can someone please explain where am i going wrong?
>>>
>>> R session info is given below:
>>>
>>> sessionInfo()
>>> R version 2.14.0 (2011-10-31)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=C LC_NAME=C
>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] grid stats graphics grDevices utils datasets
methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] cummeRbund_1.0.0 ggplot2_0.8.9 proto_0.3-9.2
reshape_0.8.4
>>> [5] plyr_1.6 RSQLite_0.10.0 DBI_0.2-5
>>>
>
>
----------------------------------------------------------------------
----------
Disclaimer\ \ \ Any views or opinions presented in
this...{{dropped:13}}
