[BioC] Unable to Generate QC Report for mogene10stv1
Rick Frausto
ricardo.frausto at sydney.edu.au
Sat Jan 8 00:56:07 CET 2011
Hi Jim,
Ok, so after doing a bit of reading and re-reading I was eventually able to
generate each page in a quartz window that the "QCReport" function should
also generate. I found which ones give me the errors. So, there should be 6
pages in total. Page 2 gives me the duplication error and page 3 gives me
the error in evaluating the argument x. The other pages are ok and are
generated as expected.
In brief, page 2 is suppose to be generated with the "signalDist(mydata)"
command. Page 3 is suppose to generated with the "plot(qc(mydata))" command.
So, I guess there must be particular requirements for these commands that
I'm missing.I've included the session below along with traceback() and
sessionInfo().
R version 2.12.0 (2010-10-15)
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ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
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[R.app GUI 1.35 (5632) x86_64-apple-darwin9.8.0]
[Workspace restored from /Users/rickfrausto/.RData]
[History restored from /Users/rickfrausto/.Rapp.history]
> library(simpleaffy)
Loading required package: affy
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: genefilter
Loading required package: gcrma
Attaching package: 'simpleaffy'
The following object(s) are masked _by_ '.GlobalEnv':
getBioC
> library(affy)
> mydata <- ReadAffy()
> eset <- rma(mydata)
Background correcting
Normalizing
Calculating Expression
> library(affycoretools); affystart(plot=T, express="rma")
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: KEGG.db
Background correcting
Normalizing
Calculating Expression
Please give the x-coordinate for a legend.30
Please give the y-coordinate for a legend.80
ExpressionSet (storageMode: lockedEnvironment)
assayData: 34760 features, 35 samples
element names: exprs
protocolData
sampleNames: A_WT1_NT_2hr.CEL B_WT1_NT_2hr.CEL ...
ZI_ST1KO_HIL6_12hr.CEL (35 total)
varLabels: ScanDate
varMetadata: labelDescription
phenoData
sampleNames: A_WT1_NT_2hr.CEL B_WT1_NT_2hr.CEL ...
ZI_ST1KO_HIL6_12hr.CEL (35 total)
varLabels: sample
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: mogene10stv1
> write.exprs(eset, file="mydata.txt")
> x <- data.frame(exprs(eset), exprs(eset_PMA), assayDataElement(eset_PMA,
"se.exprs")); x <- x[,sort(names(x))]; write.table(x, file="mydata_PMA.xls",
quote=F, col.names = NA, sep="\t")
Error in exprs(eset_PMA) :
error in evaluating the argument 'object' in selecting a method for
function 'exprs'
> mypm <- pm(mydata)
> mymm <- mm(mydata)
> myaffyids <- probeNames(mydata)
> result <- data.frame(myaffyids, mypm, mymm)
> eset; pData(eset)
ExpressionSet (storageMode: lockedEnvironment)
assayData: 34760 features, 35 samples
element names: exprs
protocolData
sampleNames: A_WT1_NT_2hr.CEL B_WT1_NT_2hr.CEL ...
ZI_ST1KO_HIL6_12hr.CEL (35 total)
varLabels: ScanDate
varMetadata: labelDescription
phenoData
sampleNames: A_WT1_NT_2hr.CEL B_WT1_NT_2hr.CEL ...
ZI_ST1KO_HIL6_12hr.CEL (35 total)
varLabels: sample
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: mogene10stv1
sample
A_WT1_NT_2hr.CEL 1
B_WT1_NT_2hr.CEL 2
C_WT1_NT_12hr.CEL 3
D_WT1_NT_12hr.CEL 4
E_WT1_HIL6_2hr.CEL 5
F_WT1_HIL6_2hr.CEL 6
G_WT1_HIL6_12hr.CEL 7
H_WT1_HIL6_12hr.CEL 8
I_FF_NT_2hr.CEL 9
J_FF_NT_2hr.CEL 10
K_FF_NT_12hr.CEL 11
L_FF_NT_12hr.CEL 12
M_FF_HIL6_2hr.CEL 13
N_FF_HIL6_2hr.CEL 14
O_FF_HIL6_12hr.CEL 15
P_FF_HIL6_12hr.CEL 16
Q_WT2_NT_2hr.CEL 17
R_WT2_NT_2hr.CEL 18
S_WT2_NT_12hr.CEL 19
T_WT2_NT_12hr.CEL 20
U_WT2_HIL6_2hr.CEL 21
V_WT2_HIL6_2hr.CEL 22
W_WT2_HIL6_12hr.CEL 23
X_WT2_HIL6_12hr.CEL 24
Y_DD_NT_2hr.CEL 25
Z_DD_NT_2hr.CEL 26
ZA_DD_NT_12hr.CEL 27
ZB_DD_NT_12hr.CEL 28
ZC_DD_HIL6_2hr.CEL 29
ZD_DD_HIL6_2hr.CEL 30
ZE_DD_HIL6_12hr.CEL 31
ZF_DD_HIL6_12hr.CEL 32
ZG_ST1KO_NT_2hr.CEL 33
ZH_ST1KO_HIL6_2hr.CEL 34
ZI_ST1KO_HIL6_12hr.CEL 35
> data.frame(eset)
X10338001 X10338003 X10338004 X10338017 X10338025
A_WT1_NT_2hr.CEL 11.71717 10.183620 9.440631 12.79412 8.823529
B_WT1_NT_2hr.CEL 11.78778 10.027760 9.489226 12.98544 8.843002
X10338026 X10338029 X10338035 X10338036 X10338037
A_WT1_NT_2hr.CEL 13.22585 9.405038 8.853564 9.379031 3.661987
B_WT1_NT_2hr.CEL 13.29043 9.575309 8.772872 9.513050 3.514885
X10338041 X10338042 X10338044 X10338047 X10338056
A_WT1_NT_2hr.CEL 10.94638 10.116516 11.88296 8.872839 3.133222
B_WT1_NT_2hr.CEL 11.23276 10.134084 12.03381 7.568584 3.088548
X10338059 X10338060 X10338063 X10338064 X10338065
JIM, I TRUNCATED THIS LIST, BUT THOUGHT IT MIGHT BE USEFUL IN DIAGNOSING THE
PROBLEMS I'M HAVING. SESSION IS CONTINUED BELOW.
> library(affyQCReport)
Loading required package: lattice
> titlePage(mydata)
[1] TRUE
> signalDist(mydata)
Warning message:
In data.row.names(row.names, rowsi, i) :
some row.names duplicated:
4,8,9,13,14,15,16,24,25,26,27,28,29,30,31,36,37,38,39,47,48,49,50,51,52,53,5
4,58,59,60,64,65,66,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,102,1
03,104,108,109,110,111,114,119,120,121,122,127,134,136,137,138,139,141,142,1
47,148,149,152,153,156,157,158,159,162,163,164,165,166,167,168,169,170,171,1
73,175,176,179,180,183,184,185,186,191,192,195,197,198,199,200,202,206,207,2
10,219,220,227,228,229,230,233,234,235,240,241,243,245,246,248,249,250,251,2
52,253,257,259,260,266,271,272,276,277,280,281,284,286,287,289,290,291,292,2
96,297,298,302,304,305,306,310,311,312,313,317,318,319,321,322,324,334,337,3
38,339,340,341,345,346,350,351,356,359,362,364,366,367,370,371,373,376,378,3
82,383,384,385,386,387,388,389,391,394,395,397,398,399,400,402,403,405,406,4
07,409,410,411,415,416,418,419,425,431,432,433,434,435,440,441,443,445,447,4
49,450,452,454,455,456,461,464,466,470,472,473,481,487,488,491,492,493,494,4
95,496,497,498,499,501,502,504,506,507,509,511,513,515,516,51 [...
truncated]
> plot(qc(mydata))
Error in plot(qc(mydata)) :
error in evaluating the argument 'x' in selecting a method for function
'plot'
> borderQC1(mydata)
[1] TRUE
> borderQC2(mydata)
[1] TRUE
> correlationPlot(mydata)
[1] TRUE
> titlePage(mydata)
[1] TRUE
> titlePage(mydata)
Error in polygon(c(0, 0, 0.9, 0.9, 0), c(0.05, 0.95, 0.95, 0.05, 0.05)) :
plot.new has not been called yet
> correlationPlot(mydata)
[1] TRUE
> titlePage(mydata)
Error in polygon(c(0, 0, 0.9, 0.9, 0), c(0.05, 0.95, 0.95, 0.05, 0.05)) :
plot.new has not been called yet
In addition: Warning message:
Display list redraw incomplete
> borderQC1(mydata)
[1] TRUE
> titlePage(mydata)
[1] TRUE
> titlePage(mydata)
Error in polygon(c(0, 0, 0.9, 0.9, 0), c(0.05, 0.95, 0.95, 0.05, 0.05)) :
plot.new has not been called yet
> traceback()
2: polygon(c(0, 0, 0.9, 0.9, 0), c(0.05, 0.95, 0.95, 0.05, 0.05))
1: titlePage(mydata)
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] affyQCReport_1.28.1 lattice_0.19-13 affycoretools_1.22.0
[4] KEGG.db_2.4.5 GO.db_2.4.5 RSQLite_0.9-4
[7] DBI_0.2-5 AnnotationDbi_1.12.0 mogene10stv1cdf_2.7.0
[10] simpleaffy_2.26.1 gcrma_2.22.0 genefilter_1.32.0
[13] affy_1.28.0 Biobase_2.10.0
loaded via a namespace (and not attached):
[1] affyio_1.18.0 affyPLM_1.26.0 annaffy_1.22.0
[4] annotate_1.28.0 biomaRt_2.6.0 Biostrings_2.18.2
[7] Category_2.16.0 GOstats_2.16.0 graph_1.28.0
[10] grid_2.12.0 GSEABase_1.12.2 IRanges_1.8.7
[13] limma_3.6.9 preprocessCore_1.12.0 RBGL_1.26.0
[16] RColorBrewer_1.0-2 RCurl_1.4-3 splines_2.12.0
[19] survival_2.36-2 tools_2.12.0 XML_3.2-0
[22] xtable_1.5-6
>
On 7/01/11 12:47 PM, "James W. MacDonald" <jmacdon at med.umich.edu> wrote:
> Hi Rick,
>
> What happens if you load the simpleaffy package first?
>
> Best,
>
> Jim
>
> On 1/7/2011 2:14 PM, Rick Frausto wrote:
>> Hi James,
>>
>> Below is the information that you requested - traceback() and sessioninfo().
>> Doesn't seem like much to me, but perhaps you can help. As you answer to a
>> lot of e-mails, thought I'd remind you that this is in regards to the "some
>> row.names duplicated" error.
>>
>> Hope your holidays were good!
>>
>> -Rick
>>
>> [R.app GUI 1.35 (5632) x86_64-apple-darwin9.8.0]
>>
>> [Workspace restored from /Users/rickfrausto/.RData]
>> [History restored from /Users/rickfrausto/.Rapp.history]
>>
>>> library(affy)
>> Loading required package: Biobase
>>
>> Welcome to Bioconductor
>>
>> Vignettes contain introductory material. To view, type
>> 'openVignette()'. To cite Bioconductor, see
>> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>>
>>> mydata<- ReadAffy()
>>> eset<- rma(mydata)
>> Background correcting
>> Normalizing
>> Calculating Expression
>>> write.exprs(eset, file="mydata.txt")
>>> mypm<- pm(mydata)
>>> mymm<- mm(mydata)
>>> myaffyids<- probeNames(mydata)
>>> result<- data.frame(myaffyids, mypm, mymm)
>>> library(affyQCReport); QCReport(mydata, file="ExampleQC.pdf")
>> Loading required package: lattice
>> Warning message:
>> In data.row.names(row.names, rowsi, i) :
>> some row.names duplicated:
>> 4,8,9,13,14,15,16,24,25,26,27,28,29,30,31,36,37,38,39,47,48,49,50,51,52,53,5
>> 4,58,59,60,64,65,66,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,102,1
>> 03,104,108,109,110,111,114,119,120,121,122,127,134,136,137,138,139,141,142,1
>> 47,148,149,152,153,156,157,158,159,162,163,164,165,166,167,168,169,170,171,1
>> 73,175,176,179,180,183,184,185,186,191,192,195,197,198,199,200,202,206,207,2
>> 10,219,220,227,228,229,230,233,234,235,240,241,243,245,246,248,249,250,251,2
>> 52,253,257,259,260,266,271,272,276,277,280,281,284,286,287,289,290,291,292,2
>> 96,297,298,302,304,305,306,310,311,312,313,317,318,319,321,322,324,334,337,3
>> 38,339,340,341,345,346,350,351,356,359,362,364,366,367,370,371,373,376,378,3
>> 82,383,384,385,386,387,388,389,391,394,395,397,398,399,400,402,403,405,406,4
>> 07,409,410,411,415,416,418,419,425,431,432,433,434,435,440,441,443,445,447,4
>> 49,450,452,454,455,456,461,464,466,470,472,473,481,487,488,491,492,493,494,4
>> 95,496,497,498,499,501,502,504,506,507,509,511,513,515,516,51 [...
>> truncated]
>> Error in plot(qc(object)) :
>> error in evaluating the argument 'x' in selecting a method for function
>> 'plot'
>>> traceback()
>> 2: plot(qc(object))
>> 1: QCReport(mydata, file = "ExampleQC.pdf")
>>> sessionInfo()
>> R version 2.12.0 (2010-10-15)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] affyQCReport_1.28.1 latptice_0.19-13 mogene10stv1cdf_2.7.0
>> [4] affy_1.28.0 Biobase_2.10.0
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.18.0 affyPLM_1.26.0 annotate_1.28.0
>> [4] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5
>> [7] gcrma_2.22.0 genefilter_1.32.0 grid_2.12.0
>> [10] IRanges_1.8.7 preprocessCore_1.12.0 RColorBrewer_1.0-2
>> [13] RSQLite_0.9-4 simpleaffy_2.26.1 splines_2.12.0
>> [16] survival_2.36-2 tools_2.12.0 xtable_1.5-6
>>>
>>
>>
>>
>>
>> On 20/12/10 6:33 AM, "James W. MacDonald"<jmacdon at med.umich.edu> wrote:
>>
>>> Hi Rick,
>>>
>>> On 12/17/2010 9:24 PM, Rick Frausto wrote:
>>>> Hey Jim,
>>>>
>>>> Ok, I will give that a go. The only problem is an ExpressionSet contains
>>>> all
>>>> of the necessary information for further analysis (e.g. phenodata,
>>>> featuredata and annotation, etc - including, treatment type, cell type,
>>>> time
>>>> points, replicates). I am still learning how to include all of these for a
>>>> complete ExpressionSet. As a starting point I've loaded a txt file
>>>> containing some of this information (gene abbrev, ontology, probeset ID)
>>>> which I created using Affymetrix's Expression Console software, without
>>>> replicate, time point and cell type info. Doing this I've gotten as far as
>>>> creating a minimal ExpressionSet, which I guess the functions you mention
>>>> below do just that but with the information contained in the CEL file only.
>>>>
>>>> In any case, since as you say, the functions in the online manual create a
>>>> proper ExpressionSet why would I get the issue of duplication?
>>>
>>> Oh yeah, the original question ;-D. Try running QCreport() again, and
>>> when it errors out run traceback() and send the output. Also include the
>>> output of sessionInfo().
>>>
>>> Jim
>>>
>>>
>>>>
>>>> In regards to the 64-bit discussion. It may have very well made enough of a
>>>> difference as it did not come up with the memory error the last time I
>>>> tried
>>>> it. Going to upgrade to 8GB RAM anyways, can't hurt.
>>>>
>>>> Cheers,
>>>> Rick
>>>>
>>>>
>>>> On 17/12/10 7:20 AM, "James W. MacDonald"<jmacdon at med.umich.edu> wrote:
>>>>
>>>>> Hi Rick,
>>>>>
>>>>> On 12/16/2010 4:13 PM, Rick Frausto wrote:
>>>>>> Hi Jim,
>>>>>>
>>>>>> How do I run an RMA analysis without a proper ExpresionSet? Honest
>>>>>> answer,
>>>>>> I
>>>>>> don't know, I just put in a command line from a manual I found online and
>>>>>> it
>>>>>> spit out some result- see #3 Affy packages in following link (
>>>>>> http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#biocon_intro).
>>>>>
>>>>> You are mistaken. All of the functions mentioned there result in a
>>>>> proper ExpressionSet. And if you just do
>>>>>
>>>>> abatch<- ReadAffy()
>>>>> eset<- rma(abatch)
>>>>>
>>>>> Then you will 100% surely get an ExpressionSet.
>>>>>
>>>>>>
>>>>>> Perhaps you don't need an ExpressionSet until after the preprocessing, at
>>>>>> least that is what I get from the "An Introduction to Bioconductor's
>>>>>> ExpressionSet Class" written by Seth Falcon, Martin Morgan and Robert
>>>>>> Gentleman. Everything seemed to be going smoothly until I tried to get a
>>>>>> QC
>>>>>> Report.
>>>>>>
>>>>>> Now, the answer for why I would want to do such a thing is easy. Simply
>>>>>> that
>>>>>> I don't know any better :) Just started working with R a few days ago,
>>>>>> but
>>>>>> I'm learning.
>>>>>>
>>>>>>
>>>>>> Apparently Snow Leopard running on 32bit can only utilize about 3.2GB of
>>>>>> RAM, whereas 64bit can make use of all 4GB. I'll switch to the 64 bit OS
>>>>>> and
>>>>>> see if it makes a difference.
>>>>>
>>>>> Well, it won't be much different. The reason a 32-bit OS can only use
>>>>> about 3.2 Gb of RAM is that the OS needs some to run. The 64-bit OS also
>>>>> needs to use some RAM, so you won't get all 4 Gb there either. The issue
>>>>> is how much RAM can be allocated to a single process, and on a 64-bit OS
>>>>> that gets bumped up significantly.
>>>>>
>>>>> Best,
>>>>>
>>>>> Jim
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> Thanks for your insight!
>>>>>>
>>>>>> Cheers,
>>>>>> Rick
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 16/12/10 11:31 AM, "James W. MacDonald"<jmacdon at med.umich.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Rick,
>>>>>>>
>>>>>>> On 12/16/2010 12:57 PM, Rick Frausto wrote:
>>>>>>>> Thanks Jim! How much memory would I need, I currently have 4GB, but
>>>>>>>> have
>>>>>>>> quite a few other programs running in the background...I'll see if
>>>>>>>> closing
>>>>>>>> them helps. Perhaps setting up an "ExpressionSet" would solve the
>>>>>>>> problem.
>>>>>>>> I
>>>>>>>> just started reading up on how to set one of these up yesterday. Will
>>>>>>>> do
>>>>>>>> this and see if the duplicates will go away.
>>>>>>>>
>>>>>>>> The "mydata" originates from CEL files and then I run the RMA analysis
>>>>>>>> on
>>>>>>>> it, but I didn't actually set up a proper ExpressionSet. I'm guessing
>>>>>>>> that
>>>>>>>> doing this might reduce the QCReport PDF file size quite considerably
>>>>>>>> since
>>>>>>>> I won't have any duplication and will make further analysis easier.
>>>>>>>
>>>>>>> How do you run an RMA analysis without setting up a proper
>>>>>>> ExpressionSet? The default behavior is to create one. In addition, why
>>>>>>> would you want to do such a thing? The ExpressionSet class is
>>>>>>> specifically designed to contain these sorts of data.
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> I'm running Snow Leopard OSX which can be set up as 64bit. Would
>>>>>>>> running
>>>>>>>> as
>>>>>>>> 64bit still necessitate more RAM?
>>>>>>>
>>>>>>> Probably. The difference isn't efficiency, but the ability to address
>>>>>>> more RAM. A 32-bit OS can still address all the available memory that
>>>>>>> you will have with just 4 Gb RAM, so you need to bump that up if you
>>>>>>> want to do all the chips together. As for how much, I don't know. Since
>>>>>>> RAM isn't that expensive these days, you might look at maxing your box
>>>>>>> out.
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Jim
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> Thanks again,
>>>>>>>> Rick
>>>>>>>>
>>>>>>>>
>>>>>>>> On 15/12/10 7:45 AM, "James W. MacDonald"<jmacdon at med.umich.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi Rick,
>>>>>>>>>
>>>>>>>>> On 12/14/2010 3:55 PM, Rick Frausto wrote:
>>>>>>>>>> Dear All,
>>>>>>>>>>
>>>>>>>>>> I have recently entered the world of R. Through some trial and error
>>>>>>>>>> I'm
>>>>>>>>>> becoming more familiar with R and the relevant Bioconductor Affy
>>>>>>>>>> packages.
>>>>>>>>>> I¹m a molecular and cell biologist with rudimentary statistical
>>>>>>>>>> knowledge
>>>>>>>>>> and even less knowledge with respect to R.
>>>>>>>>>>
>>>>>>>>>> When I enter the following:
>>>>>>>>>>
>>>>>>>>>> library(affyQCReport); QCReport(mydata, file="ExampleQC.pdf")
>>>>>>>>>>
>>>>>>>>>> I get some errors in return.
>>>>>>>>>>
>>>>>>>>>> Loading required package: lattice
>>>>>>>>>> Error: cannot allocate vector of size 437.4 Mb
>>>>>>>>>
>>>>>>>>> This indicates that you need more RAM, as you are running out of
>>>>>>>>> memory.
>>>>>>>>>
>>>>>>>>>> In addition: Warning message:
>>>>>>>>>> In data.row.names(row.names, rowsi, i) :
>>>>>>>>>> some row.names duplicated:
>>>>>>>>>>
>>>>>> 4,8,9,13,14,15,16,24,25,26,27,28,29,30,31,36,37,38,39,47,48,49,50,51,52,5
>>>>>> 3,
>>>>>>>>
>>>>>>>>
>>>>>> 5
>>>>>>>>>>
>>>>>> 4,58,59,60,64,65,66,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,10
>>>>>> 2,
>>>>>>>>
>>>>>>>>
>>>>>> 1
>>>>>>>>>>
>>>>>> 03,104,108,109,110,111,114,119,120,121,122,127,134,136,137,138,139,141,14
>>>>>> 2,
>>>>>>>>
>>>>>>>>
>>>>>> 1
>>>>>>>>>>
>>>>>> 47,148,149,152,153,156,157,158,159,162,163,164,165,166,167,168,169,170,17
>>>>>> 1,
>>>>>>>>
>>>>>>>>
>>>>>> 1
>>>>>>>>>>
>>>>>> 73,175,176,179,180,183,184,185,186,191,192,195,197,198,199,200,202,206,20
>>>>>> 7,
>>>>>>>>
>>>>>>>>
>>>>>> 2
>>>>>>>>>>
>>>>>> 10,219,220,227,228,229,230,233,234,235,240,241,243,245,246,248,249,250,25
>>>>>> 1,
>>>>>>>>
>>>>>>>>
>>>>>> 2
>>>>>>>>>>
>>>>>> 52,253,257,259,260,266,271,272,276,277,280,281,284,286,287,289,290,291,29
>>>>>> 2,
>>>>>>>>
>>>>>>>>
>>>>>> 2
>>>>>>>>>>
>>>>>> 96,297,298,302,304,305,306,310,311,312,313,317,318,319,321,322,324,334,33
>>>>>> 7,
>>>>>>>>
>>>>>>>>
>>>>>> 3
>>>>>>>>>>
>>>>>> 38,339,340,341,345,346,350,351,356,359,362,364,366,367,370,371,373,376,37
>>>>>> 8,
>>>>>>>>
>>>>>>>>
>>>>>> 3
>>>>>>>>>>
>>>>>> 82,383,384,385,386,387,388,389,391,394,395,397,398,399,400,402,403,405,40
>>>>>> 6,
>>>>>>>>
>>>>>>>>
>>>>>> 4
>>>>>>>>>>
>>>>>> 07,409,410,411,415,416,418,419,425,431,432,433,434,435,440,441,443,445,44
>>>>>> 7,
>>>>>>>>
>>>>>>>>
>>>>>> 4
>>>>>>>>>>
>>>>>> 49,450,452,454,455,456,461,464,466,470,472,473,481,487,488,491,492,493,49
>>>>>> 4,
>>>>>>>>
>>>>>>>>
>>>>>> 4
>>>>>>>>>> 95,496,497,498,499,501,502,504,506,507,509,511,513,515,516,51 [...
>>>>>>>>>> truncated]
>>>>>>>>>
>>>>>>>>> What exactly is 'mydata', and how did you generate it? The above error
>>>>>>>>> indicates that you have duplicate row names, which IIRC isn't possible
>>>>>>>>> to do with an expressionSet.
>>>>>>>>>
>>>>>>>>>> R(9062,0xa05c5540) malloc: *** mmap(size=458665984) failed (error
>>>>>>>>>> code=12)
>>>>>>>>>> *** error: can't allocate region
>>>>>>>>>> *** set a breakpoint in malloc_error_break to debug
>>>>>>>>>> R(9062,0xa05c5540) malloc: *** mmap(size=458665984) failed (error
>>>>>>>>>> code=12)
>>>>>>>>>> *** error: can't allocate region
>>>>>>>>>> *** set a breakpoint in malloc_error_break to debug
>>>>>>>>>
>>>>>>>>> More lack of memory errors.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Error in help(dt[i], package = pkg[i], htmlhelp = TRUE) :
>>>>>>>>>> unused argument(s) (htmlhelp = TRUE)
>>>>>>>>>> In addition: Warning messages:
>>>>>>>>>> 1: In data(package = .packages(all.available = TRUE)) :
>>>>>>>>>> datasets have been moved from package 'base' to package
>>>>>>>>>> 'datasets'
>>>>>>>>>> 2: In data(package = .packages(all.available = TRUE)) :
>>>>>>>>>> datasets have been moved from package 'stats' to package
>>>>>>>>>> 'datasets'
>>>>>>>>>> starting httpd help server ... done
>>>>>>>>>>
>>>>>>>>>> Would someone be able to diagnose the problem and suggest a solution?
>>>>>>>>>
>>>>>>>>> First, get more RAM. Second, you will be better off using a 64-bit OS.
>>>>>>>>> Depending on your hardware, you might be able to just install a 64-bit
>>>>>>>>> version of R.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>>
>>>>>>>>> Jim
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> If it is useful, I am using the following R software: R for Mac OS X
>>>>>>>>>> GUI
>>>>>>>>>> 1.35-dev Leopard build 32-bit. If there is any other info that would
>>>>>>>>>> be
>>>>>>>>>> useful please let me know.
>>>>>>>>>>
>>>>>>>>>> I had a read of the AffyQCReport Package pdf and I have added the
>>>>>>>>>> following
>>>>>>>>>> line: QCReport(ReadAffy(widget=TRUE)). Then I tried
>>>>>>>>>> library(affyQCReport);
>>>>>>>>>> QCReport(mydata, file="ExampleQC.pdf") again. It now seems to be
>>>>>>>>>> doing
>>>>>>>>>> something, in other words it doesn¹t go to the error, yet, but it¹s
>>>>>>>>>> been
>>>>>>>>>> processing for about 10 minutes. I am analyzing 35 chips.
>>>>>>>>>>
>>>>>>>>>> Perhaps it would work if I tried to generate each QCReport page
>>>>>>>>>> separately
>>>>>>>>>> rather than as a whole.
>>>>>>>>>>
>>>>>>>>>> Cordially,
>>>>>>>>>> Rick
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> 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
>>>>>>>>
>>>>>>
>>>>
>>
--
Rick Frausto
PhD Candidate
The University of Sydney
School of Molecular Bioscience G08
Camperdown, NSW 2006 AUSTRALIA
ricardo.frausto at sydney.edu.au
Phone: 61 2 9036 5354
Lab of Iain L. Campbell
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