On Fri, Jun 17, 2011 at 12:15 PM, Henrik Bengtsson
wrote:
> Hi.
>
> On Thu, Jun 16, 2011 at 9:52 AM, Xavi Sole wrote:
>> Hi all,
>> I have successfully performed CRMAv2 on a set of ~200 Affy 6.0 samples. I
>> have tumor and normal samples, and now I want to apply an un
Hi.
On Mon, Jun 27, 2011 at 8:37 AM, sean nj wrote:
> Hi guys,
>
> I am new to the aroma package and today I just followed the instuction on
> Henrik et al's Feb 18, 2008 paper
This is "H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed,
Estimation and assessment of raw copy numbers at the sing
Hi.
On Sun, Jun 26, 2011 at 6:00 PM, Dario Strbenac wrote:
> Hello,
>
> The append function works in a strange way because it modifies its
> first argument, as well as the result variable. Unusual for R, anyway.
Yes, most "aroma" objects are basically reference variables. This is
one of the rea
quot; "Resistant-vs-HapMap" "Resistant-vs-HapMap"
>
>> setAlias(ce,names);
>> Error in list(`setAlias(ce, names)` = , `setAlias.Explorer(ce,
>> names)` = , :
>
> [2011-06-21 09:14:47] Exception: Number of elements in argument
> '
Hi Maria.
On Wed, Jul 6, 2011 at 5:59 AM, Maria Rodrigo-Domingo wrote:
> Hi all,
>
> I am using aroma.affymetrix for an analysis on Human Exon Array data
> and would need to access the individual probe intensities mapped to
> probe_id after background correction and normalization. Is there an
> e
Hi Ying.
On Fri, Jul 8, 2011 at 10:51 AM, sean nj wrote:
> I do not know why, but after I converted the custom CDF into binary
> CDF and used the binary CDF to do analysis, the analysis went smoothly
> without any error message.
Yes, that is/was the cause of your problem. Converting text-based
Hi.
On Fri, Jul 8, 2011 at 7:33 AM, sean nj wrote:
> Hi guys,
>
> I am new to the aroma.affymetrix package.
[snip]
> One more question, is there a Vignette/instruction to illustrate the
> further gene expression analysis (high-level analysis?) using the
> output of aroma.affymetrix's RMA analys
Hi.
On Mon, Jul 11, 2011 at 5:33 AM, Anita wrote:
> Dear group,
>
> I would like to extract a data.frame on the exon level and followed
> these commands (see below), surprisingly the data.frame had these
> dimensions:
>
> 326983 249
>
> while I expected to have a data.frame with
> 1.4 Mill 249 sa
ays to NGS and that's
> why the individual probes are so important for me. So my question is
> whether it is possible to perform an analysis at the "sequence level".
To " perform an analysis at the "sequence level" " is rather vague -
it sounds like a resear
Hi.
On Sun, Jul 10, 2011 at 10:03 PM, Jill wrote:
> Also, I noticed in the affxparser library the readCel has the value of
> NULL for indices. Could that be part of the problem?
>
> readCel(filename,
> indices = NULL,
> readHeader = TRUE,
> readXY = FALSE, readIntensities = T
Before anything else, what does:
> library("affxparser");
> sessionInfo();
report?
/Henrik
PS. This is really a question for the Bioconductor list, because it is
an 'affxparser' question and independent of the aroma framework, but
let's deal with it here this time.
On Wed, Jul 13, 2011 at 11:5
kages:
> [1] stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] affxparser_1.24.0
>
>
> On Jul 13, 3:03 pm, Henrik Bengtsson project.org> wrote:
>> Before anything else, what does:
>>
>> > library("
ik
PS. I would agree that affxparser should not core dump here. However,
it is a rather particular file format error and the core dump occurs
in the Affymetrix Fusion SDK code that affxparser utilizes and there
is little we can to protect against this in affxparser.
>
>
>
> On Jul 13,
7; of read.table(), because I
think it is when you read your file back in you get the conversion.
The file itself is probably correct.
Hope this helps
/Henrik
>
>
> Thanks a lot,
>
> Ying
>
> On Jul 9, 10:09 pm, Henrik Bengtsson project.org> wrote:
>> Hi.
>
Hi.
On Wed, Aug 10, 2011 at 9:13 PM, Matthew Weiser
wrote:
> Hi,
>
> I have run into a problem reading .cel files with aroma.affymetrix. I
> am attempting to read in just a single .cel file - this was originally
> in binary format (v4), but after downloading the HuEx-1_0-st-v2.cdf
> file from the
Hi,
sorry for the delay. This should work, but before diving into serious
troubleshooting, could you please report your sessionInfo() so we know
which versions of packages etc you are using?
/Henrik
On Wed, Aug 17, 2011 at 4:38 AM, feugeas jean-paul
wrote:
> Hello,
> I am currently trying to a
Hi,
could you please us know what your sessionInfo() reports after
library(aroma.affymetrix) is called, or even, better after you get the
error? That will be key to troubleshooting this.
/Henrik
On Wed, Aug 24, 2011 at 11:00 PM, DGoode wrote:
> Hi, I'm a new user of aroma.affymetrix. I run int
Hi,
I think the answer is that MoGene-1_0-st-v1,r3.cdf was created
directly from the unofficial Affymetrix ASCII CDF using convertCdf(),
as explained on http://aroma-project.org/chipTypes/MoGene-1_0-st-v1/,
whereas you creating a CDF based on the annotation available in a
Bioconductor Platform Des
Hi,
seeing these error messages, my best guess is that those CEL files
with DAT headers containing only ".1sq" instead of the expected
"GenomeWideSNP_6.1sq" are somehow corrupt and not real GenomeWideSNP_6
CEL files. To be sure I need to study such a file. Would you mind
making one of the ".1sq"
DBI_0.2-5 genefilter_1.30.0
> [7] IRanges_1.6.17 preprocessCore_1.10.0 RSQLite_0.9-4
> [10] splines_2.11.0 survival_2.35-8 tools_2.11.0
> [13] xtable_1.5-6
>
>>
>
>
> - Message d'origine -
> De: Henrik Ben
ached packages:
> [1] aroma.affymetrix_2.1.6 affxparser_1.24.0
> aroma.apd_0.2.0
> [4] R.huge_0.3.0 aroma.core_2.1.4
> aroma.light_1.20.0
> [7] matrixStats_0.2.2 R.rsp_0.6.2
> R.cache_0.4.3
> [10] R.filesets_1.1.0 digest_0.5.0
> R.utils_1.7.8
> [13] R.oo_
0080710 22:47:02
> PDTAffymetrix platform>GenomeWideSNP_6 chipType>GenomeWideSNP_6.probe_tab filename>341479928
> 2037c033c09fd8f7c06bd042a77aef15 srcFile>
> GenomeWideSNP_6.CN_probe_tab96968290 filesize>
> 3dc2d3178f5eafdbea9c8b6eca88a89c
> Chip type: GenomeWideSNP_
/Test,set,Data/GenomeWideSNP_6/
> COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042.CEL
> File size: 65.85 MB (69053496 bytes)
> RAM: 0.01 MB
> File format: v4 (binary; XDA)
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
> Timestamp: 2008-07-13 15:02:08
>
>
> On
Hi again,
On Sat, Aug 27, 2011 at 5:22 PM, Henrik Bengtsson
wrote:
> Hi,
>
> seeing these error messages, my best guess is that those CEL files
> with DAT headers containing only ".1sq" instead of the expected
> "GenomeWideSNP_6.1sq" are somehow corrupt and n
t;);
and I think you can also analyze those problematic CEL files.
Hope this solved your problem
Henrik
On Sat, Aug 27, 2011 at 5:22 PM, Henrik Bengtsson
wrote:
> Hi,
>
> seeing these error messages, my best guess is that those CEL files
> with DAT headers containing only ".1sq&
Hi,
thanks for this. The issue with the trim() clash with IRanges was
(supposed to be) dealt with in aroma.core v1.0.6 [2009-05-14]:
o BUG FIX: Now aroma.core works with the IRanges and grid packages,
regardless on the order they were loaded.
and the comments in the code show that this especi
Hi,
aroma.affymetrix v2.2.0 et al. have been released. Make sure to update:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
The main updates are (with full details below):
FEATURES:
o Added extractExpressionSet() for ChipEffectSet.
o Instead of just throwing "Fail
aroma.light_1.20.0 matrixStats_0.2.2
> [11] R.rsp_0.6.2 R.cache_0.5.1 R.filesets_1.1.0
> digest_0.5.0 R.utils_1.7.8
> [16] R.oo_1.8.1 R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.11.10 Bios
Hi,
On Thu, Sep 15, 2011 at 9:32 AM, rahul wrote:
> I have generated a custom CDF file. When i try reading the cel files
> using the custom CDF file, I get the following error:
does it work when you use the default/regular CDF?
/Henrik
>
>
> Error in list(`AffymetrixCelSet$byName("GBM_TCGA", c
-1_0-st-v2";
cdf <- AffymetrixCdfFile$byChipType(chipType);
print(cdf);
ds <- AffymetrixCelSet$byName("Dataset1", cdf=cdf);
print(ds);
cdfC <- AffymetrixCdfFile$byChipType(chipType, tag="uniqueprobes");
print(cdfC);
setCdf(ds, cdfC);
print(ds);
/Henrik
>
> Rahul
>
x27;",
> getChipType
> at throw("Cannot set CDF. The specified CDF structure ('",
> getChipType(cdf), "
> at setCdf.AffymetrixCelSet(ds, cdfC)
> at setCdf(ds, cdfC)
>
> On Sep 15, 12:35 pm, Henrik Bengtsson project.org> wrote:
>> On Thu, Sep 15
Hi.
On Wed, Sep 21, 2011 at 9:04 AM, Tarca, Adi wrote:
>
> Hi all,
> I am processing some affymetrix exon arrays and trying to compute FIRMA
> scores. I did this for all CEL files and now I just want to exclude some CEL
> files from the analysis without removing them from the rawData folder
>
Hi.
On Sat, Sep 17, 2011 at 5:37 AM, marco wrote:
> Dear Madam or Sir
> Is there any way in aroma.affymetrix for measuring how well a gene
> is detected for human exon 1.0 ST array and human Gene 1.0 ST array? I
> mean method with same function as paCalls() in package oligo.
Unfortunately, ther
Hi,
I'm not a expert on exon analysis, but I'll try to answer some of your
questions.
On Tue, Sep 13, 2011 at 5:45 AM, rene.rotterdam
wrote:
> Dear all,
>
> I fairly new to the field of Exon Arrays and my experiences with
> Microarrays in general are quite limited, so I have a couple of
> questi
Hi,
the solution to this problem is to filter out the PCR fragments by
length that you wish the fragment-length normalization step should
utilize, e.g.
ds <- doASCRMAv2("MEFa_1", chipType="MOUSEDIVm520650", lengthRange=c(450,2000))
For more background, see:
[1] Post 'aroma.affymetrix v2.0.0 rel
Hi.
On Wed, Sep 7, 2011 at 10:53 AM, Richard Beyer wrote:
> Hi,
>
> I'm hoping someone can give me a little guidance for an unusual
> normalization need. I have 9 affy human ST arrays that have varying amounts
> of RNA, so I can't use the standard quantile normalizaton approach. The wet
> lab p
bine several analysis methods without having to
> rerun RMA for every single one of them, as they all have their own
> object class.
Sorry, at least not via the Aroma framework.
/Henrik
>
> Thank you very much in advance,
>
> Rene
>
> On Sep 21, 9:14 pm, Henrik Bengtsson proj
Hi.
On Mon, Oct 3, 2011 at 10:00 AM, Rico.Daniel wrote:
> Hello, I am trying "Naive genotyping" with MOUSEDIVm520650 arrays. I am
> following the vignette
Which one?
> and get the following error:
>
>> gender <- callXXorXY(betaN[is23], betaN[is24], adjust=adjust, from=0, to=1);
> Error in list
Hi.
On Thu, Oct 6, 2011 at 2:36 PM, Johan Staaf wrote:
> Hi Henrik
> I have come across a problem loading Affymetrix 6.0 CEL files using the
> AffymetrixCelSet$byName function as described below on a unix 64-bit
> machine.
>
> Interestingly, the same code has worked before on the same machine wit
;> cdf
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.cdf
> Filesize: 470.44MB
> Chip type: GenomeWideSNP_6,Full
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number o
Hi.
On Mon, Oct 10, 2011 at 9:01 AM, rahul wrote:
> Hello Henrik,
>
> I am using the follwing commands to process my data.
>
> library(aroma.affymetrix)
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType, tag="web,
ks
>
> Rahul
>
>
>
> On Sep 15, 1:03 pm, rahul wrote:
>> Thanks a lot for the immediate reply. I got your point, I will fix my
>> CDF and try again.
>>
>> Thank you,
>>
>> Rahul
>>
>> On Sep 15, 12:57 pm, Henrik Bengtsson >
>
ormation. (The only place I could find it
is used, is in the bpmapCluster2Cdf() method which is only used when
building custom CDFs for tiling arrays).
/Henrik
>
> Thank you,
>
> Rahul
>
> On Oct 10, 12:17 pm, Henrik Bengtsson project.org> wrote:
>> Hi
>>
>&g
On Tue, Oct 18, 2011 at 10:59 PM, Pierre Neuvial
wrote:
> Hi Qian,
>
> I'm not sure what the warnings mean, but please see below for the error.
The warnings reporting on "In readBin(con = con, what = integer(),
size = 4, n = n, signed = FALSE, : 'signed = FALSE' is only valid for
integers of siz
Hi.
On Fri, Oct 21, 2011 at 8:15 AM, marco wrote:
> Hello Henrik and everyone else
> I currently run RMA in aroma.affymetrix on dataset GSE21034 which
> contains 179 human exon 1.0 ST arrays. i use a custom CDF,
> huex10stv2hsrefseqcdt, from brainarray. the resulting data matrix
> contains 426
igure. Also, plotting
the normal BAFs along the genome indicates something is odd with your
data.
Could it be that you're looking at, say, a tumor sample?
/Henrik
On Tue, Oct 4, 2011 at 1:57 PM, Henrik Bengtsson
wrote:
> On Tue, Oct 4, 2011 at 6:46 AM, Rico.Daniel wrote:
>> Dear Henri
o process() and fit(). Alternatively, you can just delete the
directory that contains the result files you wish to redo.
/Henrik
>
> On Oct 21, 11:24 pm, Henrik Bengtsson project.org> wrote:
>> Hi.
>>
>> On Fri, Oct 21, 2011 at 8:15 AM, marco wrote:
>> &
Hi.
On Tue, Oct 25, 2011 at 9:22 AM, Ivan Smirnov wrote:
> Hi Pierre, thanks for prompt reply, however I do have all those
> annotation files downloaded from that link, see below. Do I need to
> rename them (e.g. remove tags)?
>
> /aroma.exon: ls -l annotationData/chipTypes/GenomeWideSNP_6
> tota
7424585 2011-03-28 20:14
>> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
>> -rw-rw-r-- 1 ivan ivan 9407867 2011-03-28 20:12
>> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
>>
>> Thanks
>> Ivan
>>
>>
>>
>>
>> Henrik Bengtsson
Hi.
On Mon, Oct 31, 2011 at 6:11 PM, Ivan Smirnov wrote:
> Hello, I am stuck trying to run the script:
>
> options(echo = FALSE,digits=4)
> library(aroma.affymetrix)
> verbose <- Verbose(threshold=-8, timestamp=TRUE);
> name="pediatric_HGG"
> chipTypes <- c("Mapping250K_Nsp", "Mapping250K_Sty")
>
Hi.
On Tue, Nov 1, 2011 at 10:08 AM, Ivan Smirnov wrote:
> Hi Henrik,
> So, here is the script with added printouts as you suggested:
>
>
> options(echo = FALSE,digits=4)
> library(aroma.affymetrix)
> verbose <- Verbose(threshold=-8, timestamp=TRUE);
> name="pediatric_HGG"
> chipTypes <- c("Mappi
Hi.
On Thu, Nov 3, 2011 at 8:20 AM, wrote:
>
>
> Hello,
> I am using my SNP6.0 data to run the code in CRMA v2 vignette. The following
> step is very slow, but I couldn't find how "units" calculated here in the if
> { } was used in the following step. Would you please explain the purpose of
>
Hi,
aroma.affymetrix v2.3.0 and friends have been released. Update by running:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
The is a rather small release - the main update is that now all
aroma.* packages have a namespace. This should not affect an end user
much,
Hi.
On Fri, Nov 4, 2011 at 10:15 PM, Peter Kang wrote:
> Hello,
>
> I have a question about the CRLMM algorithm implemented in Aroma. Is
> this the CRLMM v2 algorithm?
Yes. It is implemented by porting parts of oligo as well as utilizing
existing methods in the 'oligo' package.
> It seems the
Hi Les.
On Sat, Nov 5, 2011 at 4:06 PM, Les Ander wrote:
> Hi Henrik,
> I am completely new to R and to aroma;
> I've looked here http://www.aroma-project.org/howtos
> but did not get the answer to my question.
>
> Following your excellent documents I have been able to get the
> ds <-
> doCRMAv2(
On Sat, Nov 5, 2011 at 7:19 PM, Henrik Bengtsson
wrote:
> Hi.
>
> On Fri, Nov 4, 2011 at 10:15 PM, Peter Kang wrote:
>> Hello,
>>
>> I have a question about the CRLMM algorithm implemented in Aroma. Is
>> this the CRLMM v2 algorithm?
>
> Yes. It is implem
On Mon, Nov 7, 2011 at 9:35 AM, Pierre Neuvial wrote:
> What is your sessionInfo() ?
>
> Perhaps you need to upgrade aroma.affymetrix instead, although I don't
> see why you would get this core dump.
Yes, sessionInfo() and showing that you've tried with the latest
version speeds up troubleshootin
redownloaded the cdf files from the Affy website, no difference.
> Thank you.
>
> On Mon, Nov 7, 2011 at 11:19 AM, Henrik Bengtsson
> wrote:
>>
>> On Mon, Nov 7, 2011 at 9:35 AM, Pierre Neuvial
>> wrote:
>> > What is your sessionInfo() ?
>> >
>&
Hi.
On Mon, Nov 7, 2011 at 2:07 PM, Ivan Smirnov wrote:
> Hi Henrik,
>
> so I successfully generated CN segmentation and calls for my dataset
> using GLAD (thanks for your help!),
> now, what could be the easiest way to make some kind of summary plot,
> showing frequencies and/or sum of aberratio
her attached packages:
> [1] digest_0.5.1 affxparser_1.26.1
>> hdr <- readCdfHeader(pathname);
> zsh: abort (core dumped) R
> On Mon, Nov 7, 2011 at 12:35 PM, Henrik Bengtsson
> wrote:
>>
>> Hi,
>>
>> you can still do sessionInfo() just before you
Hi.
On Tue, Nov 8, 2011 at 9:18 AM, Qian wrote:
> Dear all,
> I have followed the vignette and sample code to process CNV for SNP6.0
> chips. I have finished CBS segmentation and now am ready to visualize
> the result using ChromosomeExplorer.
> I didn't get any error message so far. After the fo
ls datasets methods
> base
>
> other attached packages:
> [1] RColorBrewer_1.0-2 DNAcopy_1.22.1
> aroma.affymetrix_1.7.0 aroma.apd_0.1.7 affxparser_1.20.0
> R.huge_0.2.0 aroma.core_1.7.0 aroma.light_1.16.1
> [9] matrixStats_0.2.2 R.rsp_0.4.0
> R
Hi,
As you may have noticed, this will also happens when you try to load
GLAD by itself in a fresh R session:
> require("GLAD")
Loading required package: GLAD
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared object
'C:/ProgramFiless/R-2.14.0/library/GLAD/libs/i3
35\n8c7ffa88bb444d953214f601bb998e51\n\n\nMapping250K_Sty.na31.annot.csv\n363323700\nf1ac266c6becac99d1a7d4d343eb2a73\n\n"
Then, does this give the error?
> ftr <- readFooter(ufl);
> str(ftr);
List of 5 $ createdOn: chr "20101007 15:15:44 PDT" $ platform : chr
"Aff
Ok, so you have rather old versions running. Start by updating the XML
package, retry and report back:
http://cran.r-project.org/web/packages/XML/index.html
Also, if it still gives and error, what does the following return:
> digest(raw)
[1] "ecfee3f93033dbbf4a25fd27195ff0e9"
/Henrik
On Fri,
Hoon, thanks for the note. Yes, there is a discrepancy in how clever
the methods are. Basically the AromaUnitCnBinarySet methods go
further in trying to figure out what annotations are needed. FYI,
contrary to data set directories, the name of the chip type directory
will never have tags, which
Hi Michelle,
I've just added vignette 'Paired parent-specific copy-number
segmentation (Paired PSCBS) (low-level API after AS-CRMAv2)':
http://aroma-project.org/vignettes/PairedPSCBS-lowlevel
See if that helps
/Henrik
On Fri, Nov 11, 2011 at 1:02 PM, Michelle wrote:
> Dear aroma community,
Hi,
yes, sorry about that error; I also discovered this bug over the
weekend. I'll try to fix it soon. In the meanwhile, replace the
process() call with:
# Write the PNG files
writeGraphs(ce_test, chromosomes=c(19,22), verbose=verbose);
# Write the regions files
pathname <- writeRegions(sm_tes
0.4.1
> R.cache_0.3.0
> [13] R.filesets_0.9.1 digest_0.4.2
> R.utils_1.6.0
> [16] R.oo_1.7.4 R.methodsS3_1.2.1
>
> If I try the readFooter command again, the error comes up still:
>
> ftr <- readFooter(ufl);
> Extra content at the end of the document
>
ch file or directory". Importing
the R.rsp namespace in the aroma.core namespace solved this.
Thanks Qian Liu for reporting on this.
Update as usual with:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
/Henrik
On Mon, Nov 14, 2011 at 9:40
Hi,
the Aroma Cell Sequence (ACS) annotation file is missing. You can
download it from here:
http://aroma-project.org/chipTypes/Mapping250K_Nsp-and-Mapping250K_Sty
/Henrik
On Tue, Nov 15, 2011 at 10:23 AM, Michelle wrote:
> Hi Henrik,
> I tested the updated code and got the error message "Ex
Hi.
On Tue, Nov 15, 2011 at 1:23 PM, Michelle wrote:
> Hi Henrik,
> I downloaded the acs annotation file and now the code works for this 250K
> dataset. However, for my SNP 6.0 data, I still get this error message
> "Exception: Could not locate a file for this chip type: GenomeWideSNP_6"
> Under
Hi,
you have to make sure that all nodes have all packages loaded and
access to all of the objects (and data files).
/Henrik
On Tue, Nov 15, 2011 at 12:19 PM, Qian wrote:
> Dear all,
>
> I am working the parameter tuning for CbsModel. Every time I re-run
> segmentation it takes long time and I
Hi.
On Wed, Nov 16, 2011 at 12:06 PM, Kai wrote:
> Hi Henrik,
>
> For GWS6 data it seems to me that they can be processed to generate
> either an "AromaUnitTotalCnBinarySet" or a "CnChipEffectSet". For
> example, codes in your vignette "Estimation of total copy numbers
> using the CRMA v2 method"
Hi.
On Wed, Nov 16, 2011 at 11:48 AM, Kai wrote:
> Hi Henrik,
>
> Is the ChromosomeExplorer able to tell which version of the reference
> genome was used in generating the copy number segments when drawing
> the chromosome plots? Or can it only display hg18 or hg19 but not
> both?
First, the loc
Hi,
I'd suggest that you use the Paired PSCBS segmentation method and the
LOH caller proposed in the PSCBS paper:
A.B. Olshen*, H. Bengtsson*, P. Neuvial, P. Spellman, R.A. Olshen,
V.E. Seshan, Parent-specific copy number in paired tumor-normal
studies using circular binary segmentation, Bioinfor
ou use mergeStrands=FALSE.
/Henrik
>
> Thanks again.
>
> Best,
> Kai
>
> On Nov 16, 5:09 pm, Henrik Bengtsson project.org> wrote:
>> Hi.
>>
>> On Wed, Nov 16, 2011 at 12:06 PM, Kai wrote:
>> > Hi Henrik,
>>
>> > For GWS6 data it seems
utils_1.6.0 R.oo_1.7.4 R.methodsS3_1.2.1
>
> Best,
> Kai
>
> On Nov 16, 5:54 pm, Henrik Bengtsson project.org> wrote:
>> Hi.
>>
>> On Wed, Nov 16, 2011 at 11:48 AM, Kai wrote:
>> > Hi Henrik,
>>
>> > Is the ChromosomeE
Hi,
I'm digging through my inbox and found this one - sorry for wait.
On Tue, Oct 18, 2011 at 12:54 PM, rahul wrote:
> Hello Henrik,
>
> I have a custom CDF for HuEx1.0stv2 and each probeset represents an
> exon. I am confused with mergeGroups option in ExonRmaPlm.
> When should we set mergeGro
Hi,
sorry for the wait.
On Fri, Oct 14, 2011 at 6:25 AM, rene.rotterdam
wrote:
> Hi everyone,
>
> I have a weird situation at the moment, as I am processing my HuEx
> chips according to your suggested script and all columns in the
> fsScores array contain -processed values. I suppose this is not
Hi.
On Tue, Oct 18, 2011 at 2:46 AM, rene.rotterdam
wrote:
> Hi everyone,
>
> in my group the question popped up whether it is possible to perform
> the FIRMA analysis on a subset of a number of samples that have been
> normalized all together.
> For example: Assume we have a data set of 6 differ
t;> ufl <- AromaUflFile$byChipType("Mapping250K_Sty", tags="na31,HB20101007");
>> ftr <- readFooter(ufl);
>> str(ftr);
> List of 5
> $ createdOn: chr "20101007 15:15:44 PDT"
> $ platform : chr "Affymetrix"
> $ chipType : chr
Hi.
On Fri, Nov 25, 2011 at 10:07 AM, evansa wrote:
> Hi,
>
> Sorry if this is dumb, I am new to microarray analysis, and
> aroma.affymetrix, and am having difficulties figuring out how data is
> structured and how to access it.
If you have specific questions/use cases on accessing data, I'll tr
Congratulations - you just won the price for the world shortest issue report ;)
Some ideas:
1. Use argument verbose=-10
2. Use traceback() when you get an error.
Other than that:
3. What is your sessionInfo()?
4. Show us your script.
/Henrik
On Tue, Nov 29, 2011 at 11:57 PM, Peiyong wrote:
>
s grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.affymetrix_2.3.0 affxparser_1.26.2 aroma.apd_0.2.0
> [4] R.huge_0.3.0 aroma.core_2.3.2 aroma.light_1.22.0
> [7] matrixStats_0.4.0 R.rsp_0.7.0 R.cache_
On Wed, Nov 30, 2011 at 2:12 PM, Henrik Bengtsson
wrote:
> Hi.
>
> NO REPLY EXPECTED
The above sentence was a mistake - seems to been added by my email
client. Feel free to reply. /H
>
>
> On Wed, Nov 30, 2011 at 12:24 AM, Peiyong wrote:
>> Thanks!
>>
>
Hi.
On Thu, Dec 1, 2011 at 12:40 PM, Steven McKinney wrote:
> Hi all,
>
> I am setting up to run analysis on Affymetrix SNP6, 250K Nsp and 250K Sty
> chip types.
> As I read through the current documentation, I've noticed the following items
> that
> may need attention, or I might need clarific
Hi.
On Wed, Nov 30, 2011 at 6:38 PM, xiaowei guan wrote:
>
> Hello Henrik,
>
> May I ask you a question about using the http://www.aroma-project.org/node/38
> Vignette to derive the gene centric values for HuGene-1_0-st-v1 array? I
> follow the command, but it only generated the probe level dat
Hi.
Yes, the Aroma framework can handle this.
On Fri, Dec 2, 2011 at 12:19 PM, Steven McKinney wrote:
> Hi all,
>
> I am running an analysis on Affymetrix SNP6, 250K Nsp and 250K Sty chip types.
> For various reasons, patient samples were assessed either on SNP6 chips or
> on 500K chipsets (250K
uidance.
>
>
> Steven McKinney
>
>
>> -Original Message-
>> From: aroma-affymetrix@googlegroups.com [mailto:aroma-
>> affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
>> Sent: December-02-11 12:49 PM
>> To: aroma-affymetrix@googlegroups.c
ily export those TCNs to tab-delimited text files using
writeDataFrame(), cf. http://aroma-project.org/howtos/writeDataFrame.
/Henrik
>
>
>
> On Thu, Dec 1, 2011 at 6:14 AM, Henrik Bengtsson
> wrote:
>>
>> On Wed, Nov 30, 2011 at 2:12 PM, Henrik Bengtsson
>> wrot
Hi.
On Tue, Dec 6, 2011 at 11:49 AM, Steven McKinney wrote:
>
>
> Hi all,
>
> Data from multiple sources is available that would in principle allow
> me to do a tumour/normal copy number analysis. The normal data was
> obtained from samples processed using Affymetrix GenomeWideSNP_6
> chips wher
Hi.
On Thu, Dec 8, 2011 at 7:01 AM, Les Ander wrote:
> Dear Henrik,
> I have a really quick question. I have obtained regions of cnv using
> cbs and
> I am unclear regarding the interpretation of the data, in particular,
> what does
> "mean" and the "count" mean? Is count the number of probes?
>
mary.
/Henrik
>
> best,
> Xiaowei
>
>
> On Thu, Dec 1, 2011 at 4:34 PM, Henrik Bengtsson
> wrote:
>>
>> Hi.
>>
>> On Wed, Nov 30, 2011 at 6:38 PM, xiaowei guan wrote:
>> >
>> > Hello Henrik,
>> >
>> > May I ask you a
Hi,
you'll find old
On Thu, Dec 8, 2011 at 12:03 PM, wisekh6 wrote:
> Dear Henrik,
> I am looking for the old na30 (hg18) annotation files for SNP6 that
> are necessary for running CRMA v2.
Not sure what you mean by "old [...] that are necessary"; you
obviously use the newer ones too.
> I don'
Hi,
On Mon, Dec 12, 2011 at 1:15 PM, Greg Wall wrote:
> CORRECTION:
>
> ref.theta <- extractMatrix(Normal)
> theta <- extractMatrix(Tumor)
> C <- 2 * theta/ref.theta
>
>
> On Mon, Dec 12, 2011 at 1:09 PM, Gregory W wrote:
>>
>> Hello,
>>
>> Many thanks for the site and quick feedba
8401618, 8826931, 9000365, ..., 9144105 [8]
> Path (to the first file):
> totalAndFracBData/TumourNormal,ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY/Mapping250K_Sty
> Total file size: 7.28 MB
> RAM: 0.01MB
>
>
>> cns <- CbsModel(sets$Tum, sets$Nor);
> Loading required package
On Tue, Dec 13, 2011 at 2:44 AM, James F. Reid
wrote:
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message
Hi.
On Tue, Dec 13, 2011 at 7:48 AM, wisekh6 wrote:
> Dear Henrik,
>
> I ran "doCRMAv2" with copy number data on the GenomeWide SNP6.0
> platform.
> For your information, all annotation files used in this run were
> downloaded from your website, and R 2.13.0 was loaded.
>
> This run generated a w
Hi,
what is your sessionInfo() and what does your R script look like?
/Henrik
On Thu, Dec 15, 2011 at 4:32 AM, Zelha Nil wrote:
> Hi Henrik,
>
> There is a problem in creating regions.xls file, does not form at the end
> of the segmentation. Therefore, I could not get any plots, heatmaps,
> d
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