Hi list,
I ran into a problem using chipAlongChrom to visualize a Chip chip
array
intensities:
> chipAlongChrom(X,chrom="5", probeAnno=probeAnno,gff=mm9genes2,
xlim=c(37.63e6, 37.64e6), ylim=c(-3,5), paletteName="S
et2")
Getting probe intensities in selected regions..,
Preparing color scheme...
Plotting intensities...
Obtain genomic features...
Warning messages:
1: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff =
mm9genes2, :
The identifiers of 28 reporters in the region to plot are not found
as
'featureNames' of X
2: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff =
mm9genes2, :
Only NA values in specified region.
A plot came up and could display everything except intensity data
which are
supposed to center around the dashed zero line. This function uses
gff,
probeAnno and expression set files. What file(s) should I check, or a
script issue?
Thanks,
Jianping
##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX: (919)843-3103
E-Mail: jjin at email.unc.edu
Hello,
are the warning messages any indication what the source of the problem
might be? Does the probeAnno object that you use really correspond to
the microarray platform of your ExpressionSet "X"? Maybe you
accidentally used a probeAnno from another array platform.
Are there actually any probes mapping to this region that you wanted
to
plot. The region is selected by specifying the argument "xlim" as c
(<the start="" site="" that="" you="" want="">, <the end="" site="" that="" you="" want="">).
Try something like
table(probeAnno["5.index"] %in% featureNames(X))
to see how many probes in your probeAnno are actually defined on your
array.
Try different chromosomes and regions to figure out what is wrong.
Potentially you may have to rebuild the probeAnno object for that
array.
Regards,
Joern
PS: Please also always provide the output of sessionInfo() when asking
questions on this list, so we can figure out if outdated or
conflicting
versions of certain packages could be a source of problems.
Jianping Jin wrote:
> Hi list,
>
> I ran into a problem using chipAlongChrom to visualize a Chip chip
> array intensities:
>
>> chipAlongChrom(X,chrom="5", probeAnno=probeAnno,gff=mm9genes2,
> xlim=c(37.63e6, 37.64e6), ylim=c(-3,5), paletteName="S
> et2")
> Getting probe intensities in selected regions..,
> Preparing color scheme...
> Plotting intensities...
> Obtain genomic features...
> Warning messages:
> 1: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff =
> mm9genes2, :
> The identifiers of 28 reporters in the region to plot are not found
> as 'featureNames' of X
>
> 2: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff =
> mm9genes2, :
> Only NA values in specified region.
>
> A plot came up and could display everything except intensity data
> which are supposed to center around the dashed zero line. This
> function uses gff, probeAnno and expression set files. What file(s)
> should I check, or a script issue?
>
> Thanks,
>
> Jianping
>
--
Joern Toedling
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Phone +44(0)1223 492566
Email toedling at ebi.ac.uk
Thanks for your quick reply.
> table(probeAnno["5.index"] %in% featureNames(X))
FALSE
21152
What are feature names in probeAnno? Actually I used a new output file
from
the script you edited to generate probeAnno with no complain:
probeAnno <-
posToProbeAnno("C:/from_DriveD/Chip-
chip/Bultman/allChromExonerateOut_new.txt")
Creating probeAnno mapping for chromosome 1 10 11 12 13 14 15 16
17 18
19 2 3 4 5 6 7 8 9 X Y Done.
allChrs <- chromosomeNames(probeAnno)
genome(probeAnno) <- "M. musculus (mm9)"
arrayName(probeAnno) <- "2007-02-27_MM8_CpG_Island_Pro_Tiling"
FYI
> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N
AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI
FICATION=C
attached base packages:
[1] splines tools stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] biomaRt_1.16.0 topGO_1.10.1 GO.db_2.2.5
[4] RSQLite_0.7-1 DBI_0.2-4 graph_1.20.0
[7] ccTutorial_1.0.0 Ringo_1.6.0 SparseM_0.78
[10] RColorBrewer_1.0-2 vsn_3.8.0 affy_1.20.2
[13] limma_2.16.4 geneplotter_1.20.0 annotate_1.20.1
[16] xtable_1.5-4 AnnotationDbi_1.4.2 lattice_0.17-17
[19] genefilter_1.22.0 survival_2.34-1 Biobase_2.2.1
loaded via a namespace (and not attached):
[1] affyio_1.10.1 cluster_1.11.11 grid_2.8.1
[4] KernSmooth_2.22-22 preprocessCore_1.4.0 RCurl_0.94-0
[7] XML_1.99-0
Jianping
--On Thursday, January 22, 2009 5:38 PM +0000 Joern Toedling
<toedling at="" ebi.ac.uk=""> wrote:
> Hello,
>
> are the warning messages any indication what the source of the
problem
> might be? Does the probeAnno object that you use really correspond
to
> the microarray platform of your ExpressionSet "X"? Maybe you
> accidentally used a probeAnno from another array platform.
> Are there actually any probes mapping to this region that you wanted
to
> plot. The region is selected by specifying the argument "xlim" as c
> (<the start="" site="" that="" you="" want="">, <the end="" site="" that="" you="" want="">).
>
> Try something like
>
> table(probeAnno["5.index"] %in% featureNames(X))
>
> to see how many probes in your probeAnno are actually defined on
your
> array.
>
> Try different chromosomes and regions to figure out what is wrong.
> Potentially you may have to rebuild the probeAnno object for that
array.
>
> Regards,
> Joern
>
> PS: Please also always provide the output of sessionInfo() when
asking
> questions on this list, so we can figure out if outdated or
conflicting
> versions of certain packages could be a source of problems.
>
>
> Jianping Jin wrote:
>> Hi list,
>>
>> I ran into a problem using chipAlongChrom to visualize a Chip chip
>> array intensities:
>>
>>> chipAlongChrom(X,chrom="5", probeAnno=probeAnno,gff=mm9genes2,
>> xlim=c(37.63e6, 37.64e6), ylim=c(-3,5), paletteName="S
>> et2")
>> Getting probe intensities in selected regions..,
>> Preparing color scheme...
>> Plotting intensities...
>> Obtain genomic features...
>> Warning messages:
>> 1: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff =
>> mm9genes2, :
>> The identifiers of 28 reporters in the region to plot are not
found
>> as 'featureNames' of X
>>
>> 2: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff =
>> mm9genes2, :
>> Only NA values in specified region.
>>
>> A plot came up and could display everything except intensity data
>> which are supposed to center around the dashed zero line. This
>> function uses gff, probeAnno and expression set files. What file(s)
>> should I check, or a script issue?
>>
>> Thanks,
>>
>> Jianping
>>
>
> --
> Joern Toedling
> EMBL - European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD
> United Kingdom
> Phone +44(0)1223 492566
> Email toedling at ebi.ac.uk
>
##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX: (919)843-3103
E-Mail: jjin at email.unc.edu
Jianping Jin wrote:
> table(probeAnno["5.index"] %in% featureNames(X))
>
> FALSE
> 21152
well, none of the probes seems to be included in the names of the
probes
on your arrays.
How did you create the object "X"? Can you show me the output of
str(probeAnno["5.index"])
str(probeAnno["5.start"])
str(probeAnno["5.end"])
## and for comparison:
str(probeAnno["1.index"])
str(probeAnno["1.start"])
# And what is
str(featureNames(X))
featureNames(X)[1:30]
str(X)
dim(X)
>
> What are feature names in probeAnno? Actually I used a new output
file
> from the script you edited to generate probeAnno with no complain:
>
> probeAnno <-
> posToProbeAnno("C:/from_DriveD/Chip-
chip/Bultman/allChromExonerateOut_new.txt")
>
> Creating probeAnno mapping for chromosome 1 10 11 12 13 14 15 16
17
> 18 19 2 3 4 5 6 7 8 9 X Y Done.
> allChrs <- chromosomeNames(probeAnno)
> genome(probeAnno) <- "M. musculus (mm9)"
> arrayName(probeAnno) <- "2007-02-27_MM8_CpG_Island_Pro_Tiling"
This looks alright to me. I think the function is working, but somehow
the probeAnno does not seem to match your data ExpressionSet.
Maybe can you also provide me with the first few lines of this file,
just to be sure?
C:/from_DriveD/Chip-chip/Bultman/allChromExonerateOut_new.txt
Joern
Hello,
this seems to be the source of the problem. The identifiers of the
probes that you remapped are of this form
5313_0084_0040
while in the ExpressionSet they are of the form
CHR10FS100018407
Were both these types of identifiers given in your array description
file (ndf)? If so, and if there's a one-to-one mapping between these,
you can probably use these as well as featureNames in the
ExpressionSet.
You will have to look into the raw RGList type data and see if these
identifiers of the type 5313_0084_0040 are also in there. Have a look
at
tail(RG$genes)
If so you can set these identifiers to also be the featureNames of the
ExpressionSet by changing the argument "idColumn" of the function
preprocess to this column header.
Otherwise, if the identifiers of this type 5313_0084_0040 are not
unique, you might at the moment lose information from your data, as
only
uniquely mapped probes are considered for finding enriched regions. In
this case, you will probably have to assign the correct unique
identifiers to the probe sequences in your Fasta files and you might
have to run Exonerate again in this case.
Hope this helps.
Regards,
Joern
Jianping Jin wrote:
>
>
>> str(probeAnno["5.index"])
> chr [1:21152] "5313_0084_0040" "5313_0760_0290" "5313_0060_0330" ...
>> featureNames(X)[1:30]
> [1] "CHR10FS100018407" "CHR10FS100018507" "CHR10FS100018612"
> "CHR10FS100018717"
> [5] "CHR10FS100018817" "CHR10FS100018927" "CHR10FS100019007"
> "CHR10FS100019103"
> [9] "CHR10FS100019228" "CHR10FS100019328" "CHR10FS100019428"
> "CHR10FS100019503"
> [13] "CHR10FS100019603" "CHR10FS100019703" "CHR10FS100019824"
> "CHR10FS100019927"
> [17] "CHR10FS100020027" "CHR10FS100020117" "CHR10FS010119532"
> "CHR10FS010119652"
> [21] "CHR10FS010119737" "CHR10FS010119840" "CHR10FS010119947"
> "CHR10FS010120052"
> [25] "CHR10FS010120142" "CHR10FS010120232" "CHR10FS010120343"
> "CHR10FS010120453"
> [29] "CHR10FS010120552" "CHR10FS010120652"
Hi Jianping,
I presume you created the histogram as we specified in the PLoS CB
tutorial article. The error message literally means that the object
"y0"
does not exist, and you need to create it before drawing the
histogram.
One option for creating y0, which is the variable holding the
threshold
for calling ChIP-enriched region, is also given in the tutorial as
y0 <- apply(exprs(smoothX), 2, upperBoundNull, prob=0.99)
Hope this helps.
Joern
Jianping Jin wrote:
> Thanks Joern.
>
> I re-ran Exonerate and it worked out for me.
>
> There is anther question. When I tried to find ChIP-enriched regions
> between two experiment conditions with histogram (smoothed reporter
> level[log2] versus Percent of Total) by print(h), the error messages
> on histograms of both conditions appear:
>
> Error using packet 1 (or 2) object "y0" not found.
>
> Both histograms look like normal distribution and very similar,
though
> condition one shifts a bit left around zero. This may be caused by
the
> fact that there is no mixture of two underlying distribution was
> found. I wanted to make sure if the "no object y(0) being found
itself
> is the source of the error (so I may want to try other normalization
> method) or something else I missed.
>
> Please take a look at the attached file. Appreciate your help!
>
> Jianping
>
--
Joern Toedling
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Phone +44(0)1223 492566
Email toedling at ebi.ac.uk
Hi Joern,
You are right. I need to generate y0 for the plot.
Here is another trouble:
> plot(chersX[[which.max(chersXD$maxLevel)]],smoothX,probeAnno=probeAn
no,
gff=mm9genes2, paletteName="Dark2", ylim=c(-1,6))
Error in as.double(x) :
cannot coerce type 'S4' to vector of type 'double'
chipAlongChrom works with expression data while plot works with x and
y
coordinates. How chersX can be plotted with smoothX?
thanks,
Jianping
--On Tuesday, January 27, 2009 1:47 PM +0000 Joern Toedling
<toedling at="" ebi.ac.uk=""> wrote:
> Hi Jianping,
>
> I presume you created the histogram as we specified in the PLoS CB
> tutorial article. The error message literally means that the object
"y0"
> does not exist, and you need to create it before drawing the
histogram.
> One option for creating y0, which is the variable holding the
threshold
> for calling ChIP-enriched region, is also given in the tutorial as
> y0 <- apply(exprs(smoothX), 2, upperBoundNull, prob=0.99)
> Hope this helps.
>
> Joern
>
> Jianping Jin wrote:
>> Thanks Joern.
>>
>> I re-ran Exonerate and it worked out for me.
>>
>> There is anther question. When I tried to find ChIP-enriched
regions
>> between two experiment conditions with histogram (smoothed reporter
>> level[log2] versus Percent of Total) by print(h), the error
messages
>> on histograms of both conditions appear:
>>
>> Error using packet 1 (or 2) object "y0" not found.
>>
>> Both histograms look like normal distribution and very similar,
though
>> condition one shifts a bit left around zero. This may be caused by
the
>> fact that there is no mixture of two underlying distribution was
>> found. I wanted to make sure if the "no object y(0) being found
itself
>> is the source of the error (so I may want to try other
normalization
>> method) or something else I missed.
>>
>> Please take a look at the attached file. Appreciate your help!
>>
>> Jianping
>>
>
> --
> Joern Toedling
> EMBL - European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD
> United Kingdom
> Phone +44(0)1223 492566
> Email toedling at ebi.ac.uk
>
##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX: (919)843-3103
E-Mail: jjin at email.unc.edu
Hi Joern,
I used the code on the PLos article to summarize the GO terms with the
ChIP-enriched regions. But I got some problems in sigGOTable:
NFRes <- sigGOTable(NFOnlygenes)
.
.
Level 2: 18 nodes to be scored (17 eliminated genes)
Level 1: 1 nodes to be scored (17 eliminated genes)
Error in .local(object, ...) :
Use: topGOdata, topGOresult_1, topGOresult_2, ..., "parameters".
What is the problem and can we fix it?
thanks,
Jianping
--On Tuesday, January 27, 2009 10:52 AM -0500 Jianping Jin
<jjin at="" email.unc.edu=""> wrote:
> Hi Joern,
>
> You are right. I need to generate y0 for the plot.
>
> Here is another trouble:
>
>> plot(chersX[[which.max(chersXD$maxLevel)]],smoothX,probeAnno=probeA
nno,
> gff=mm9genes2, paletteName="Dark2", ylim=c(-1,6))
> Error in as.double(x) :
> cannot coerce type 'S4' to vector of type 'double'
>
> chipAlongChrom works with expression data while plot works with x
and y
> coordinates. How chersX can be plotted with smoothX?
>
> thanks,
>
> Jianping
>
> --On Tuesday, January 27, 2009 1:47 PM +0000 Joern Toedling
> <toedling at="" ebi.ac.uk=""> wrote:
>
>> Hi Jianping,
>>
>> I presume you created the histogram as we specified in the PLoS CB
>> tutorial article. The error message literally means that the object
"y0"
>> does not exist, and you need to create it before drawing the
histogram.
>> One option for creating y0, which is the variable holding the
threshold
>> for calling ChIP-enriched region, is also given in the tutorial as
>> y0 <- apply(exprs(smoothX), 2, upperBoundNull, prob=0.99)
>> Hope this helps.
>>
>> Joern
>>
>> Jianping Jin wrote:
>>> Thanks Joern.
>>>
>>> I re-ran Exonerate and it worked out for me.
>>>
>>> There is anther question. When I tried to find ChIP-enriched
regions
>>> between two experiment conditions with histogram (smoothed
reporter
>>> level[log2] versus Percent of Total) by print(h), the error
messages
>>> on histograms of both conditions appear:
>>>
>>> Error using packet 1 (or 2) object "y0" not found.
>>>
>>> Both histograms look like normal distribution and very similar,
though
>>> condition one shifts a bit left around zero. This may be caused by
the
>>> fact that there is no mixture of two underlying distribution was
>>> found. I wanted to make sure if the "no object y(0) being found
itself
>>> is the source of the error (so I may want to try other
normalization
>>> method) or something else I missed.
>>>
>>> Please take a look at the attached file. Appreciate your help!
>>>
>>> Jianping
>>>
>>
>> --
>> Joern Toedling
>> EMBL - European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge CB10 1SD
>> United Kingdom
>> Phone +44(0)1223 492566
>> Email toedling at ebi.ac.uk
>>
>
>
>
> ##################################
> Jianping Jin Ph.D.
> Bioinformatics scientist
> Center for Bioinformatics
> Room 3133 Bioinformatics building
> CB# 7104
> University of Chapel Hill
> Chapel Hill, NC 27599
> Phone: (919)843-6105
> FAX: (919)843-3103
> E-Mail: jjin at email.unc.edu
##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX: (919)843-3103
E-Mail: jjin at email.unc.edu
