[aroma.affymetrix] Questions on extracting probeset summaries
Hi Henrik, I was processing HG-U133_Plus_2 datasets. While extracting probeset summaries(chip effects) as a data frame, I only got 27604 objs * n variables. I was hoping to get a data frame of 54675 objs., which equals the number of units in HG-U133_Plus_2 chip. Am I missing some steps, or processing the wrong CEL files? Thanks a lot! -- -- 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 because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[aroma.affymetrix] Re: sfit
Hi, Please check old discussions. I remember there were discussions. I had the same issue. Most probably, you did not install if you were using Linux system On Wednesday, January 21, 2015 at 3:46:49 PM UTC+2, Juanjo Lozano wrote: Hi, I found Error: Package not loaded: sfit Execution halted in R version 3.1.2 (2014-10-31) -- Pumpkin Helmet Could you help-me? Best Juanjo -- -- 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 because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[aroma.affymetrix] Re: Regarding the copy number states and further processing
Hi, I have tried this and works good but at the end I need the information whether there is a gain or loss at the segment. I will use GLAD model to get gain or loss at a segment. My samples and controls are completely unrelated so I am little bit doubtful whether I am doing right or not. I also found some other algorithms that can work on segments produced by CBS model still looking into them. I think you can use GLAD to call gain and loss. But CBS does not return gain or loss, only segments. If you use CBS you should call gain or loss yourself (or use other tools such as GISTIC). Then I am also looking for CNA. What other softwares have you tried on data from CytoScan HD array? Like you I used aroma to preprocess, segmented using CBS and manually call gain or loss. The simplest way is using a threshold to define gain or loss. If I remember correctly, one of TCGA papers in Nature, there a fixed threshold was used to define gain and loss. Maybe you can check that. Br, Br, C.Y Thanks, Best Regards, Sam. On Tuesday, January 20, 2015 at 10:38:27 AM UTC+1, Chengyu Liu wrote: Hi, On Monday, January 19, 2015 at 3:42:59 PM UTC+2, Sam Padmanabhuni wrote: Dear AromaAffymetrix Team, First of all, thank you very much for such a detailed vignette on how to perform the CNV analysis. I am Sam, a PhD student in genetics, working on CNV analysis on data from CytoScan HD Array. I have read the vignette to do CRMAv2 and non-paired CBS. I have copied the commands and ran in R. But, I have few questions regarding CbsModel and GladModel in segmentation algorithm: 1. It is mentioned that, copy number states is not calculated in CbsModel segmentation. How do I get information of whether the segment is a loss or gain from output of CbsModel? I mean can this information be passed to other algorithms to estimate copy number state. As far as I know, the out put of CBS is the relative copy number. It does not directly tell you the copy number states. 2. I have looked in to GLAD model and it is mentioned that it is developed for aCGH but my data is not from aCGH. Can it be still used to calculate copy number states for the data I am working on? GLAD can calculate copy number states for affy-array, although I have not used it before. 3. Also, do you have a vignette on how to run CRMAv2 and CBS on CytoScan HD array? This would be really helpful. It is the same with other chiptype, prepare input as required (there is vignette). BTW, I am also working on CytoScan HD. What kind of analysis are you going to do? Do you have paired samples or non-paired? Maybe we have something common and we can discuss. Br, C.Y Thank you, Best, Sam. Best Regards, Sam. Best, Sam. -- -- 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 because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Questions on extracting probeset summaries
Thanks. I can *not* reproduce this, e.g.
ces
ChipEffectSet:
Name: GSE9890
Tags: GRBC,QN,RMA,oligo
Path: plmData/GSE9890,GRBC,QN,RMA,oligo/HG-U133_Plus_2
Platform: Affymetrix
Chip type: HG-U133_Plus_2,monocell
Number of arrays: 10
Names: GSM249671, GSM249672, GSM249673, ..., GSM249680 [10]
Time period: 2015-01-17 09:43:28 -- 2015-01-17 09:43:35
Total file size: 5.75MB
RAM: 0.02MB
Parameters: {}
ces[[1]]
ChipEffectFile:
Name: GSM249671
Tags: chipEffects
Full name: GSM249671,chipEffects
Pathname:
plmData/GSE9890,GRBC,QN,RMA,oligo/HG-U133_Plus_2/GSM249671,chipEffects.CEL
File size: 589.25 kB (603394 bytes)
RAM: 0.02 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: HG-U133_Plus_2,monocell
Timestamp: 2015-01-17 09:43:28
Parameters: {probeModel: chr pm}
data - extractDataFrame(ces, units=NULL, addNames=TRUE)
str(data)
'data.frame': 54675 obs. of 15 variables:
$ unitName : chr AFFX-BioB-5_at AFFX-BioB-M_at AFFX-BioB-3_at
AFFX-BioC-5_at ...
$ groupName: chr ...
$ unit : int 1 2 3 4 5 6 7 8 9 10 ...
$ group: int 1 1 1 1 1 1 1 1 1 1 ...
$ cell : int 1 2 3 4 5 6 7 8 9 10 ...
$ GSM249671: num 1614 2691 2120 3904 2238 ...
$ GSM249672: num 2612 4060 3301 5686 3280 ...
$ GSM249673: num 2876 5178 4014 6861 4050 ...
$ GSM249674: num 3328 5704 4350 7617 4505 ...
$ GSM249675: num 3101 5455 4131 7735 4560 ...
$ GSM249676: num 5081 8883 7173 10997 7188 ...
$ GSM249677: num 2329 4186 3209 5853 3482 ...
$ GSM249678: num 1723 3177 2353 5537 3141 ...
$ GSM249679: num 1442 2458 2114 4285 2370 ...
$ GSM249680: num 1469 2641 2154 4583 2582 ...
So, let's start troubleshooting. First, you should see the exact same
as I do for:
cdf - getCdf(ces)
cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HG-U133_Plus_2
Filename: HG-U133_Plus_2,monocell.CDF
File size: 9.63 MB (10098009 bytes)
Chip type: HG-U133_Plus_2,monocell
RAM: 3.34MB
File format: v4 (binary; XDA)
Dimension: 246x245
Number of cells: 60270
Number of units: 54675
Cells per unit: 1.10
Number of QC units: 9
If not, that's where the problem is. If ok, then check this output:
map - getUnitGroupCellMap(cdf)
str(map) str(map)
Classes 'UnitGroupCellMap' and 'data.frame':54675 obs. of 3 variables:
$ unit : int 1 2 3 4 5 6 7 8 9 10 ...
$ group: int 1 1 1 1 1 1 1 1 1 1 ...
$ cell : int 1 2 3 4 5 6 7 8 9 10 ...
This map is essential in what information gets pulled out and
returned. The number of rows/observations in this data frame should
match the number of units in the 'cdf', i.e. 54,675 units.
Let's start with that.
Henrik
On Thu, Jan 22, 2015 at 5:00 PM, Qingzhou Zhang zqznept...@gmail.com wrote:
Hi, Henrik,
Thanks for the reply!
Here is my code:
library(aroma.affymetrix)
RawName = Project1
RawChipType = HG-U133_Plus_2
ces - doGCRMA(RawName, chipType = RawChipType)
data - extractDataFrame(ces, units = NULL, addNames = TRUE)
Here is the sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_GB.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_GB.UTF-8
LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8
LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.light_2.2.1 aroma.affymetrix_2.13.0 aroma.core_2.13.0
R.devices_2.12.0
[5] R.filesets_2.6.0R.utils_1.34.0 R.oo_1.18.2
affxparser_1.38.0
[9] R.methodsS3_1.6.2
loaded via a namespace (and not attached):
[1] aroma.apd_0.5.0base64enc_0.1-2Cairo_1.5-7digest_0.6.8
DNAcopy_1.40.0
[6] matrixStats_0.13.0 PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0
R.rsp_0.19.7
[11] tools_3.1.1
Here is the traceback()
1: extractDataFrame(ces, units = NULL, addNames = TRUE)
I tried several times, but always got a data frame containing 27604 obj. :-(
Thanks
On Friday, 23 January 2015 01:36:00 UTC+8, Henrik Bengtsson wrote:
On Thu, Jan 22, 2015 at 5:44 AM, Qingzhou Zhang zqzne...@gmail.com
wrote:
Hi Henrik,
I was processing HG-U133_Plus_2 datasets. While extracting probeset
summaries(chip effects) as a data frame, I only got 27604 objs * n
variables.
I was hoping to get a data frame of 54675 objs., which equals the number
of
units in HG-U133_Plus_2 chip. Am I missing some steps, or processing the
wrong CEL files?
Hard to say. Can you share your code (from beginning to end) showing
what you're doing?
Henrik
Thanks a lot!
--
--
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.
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Re: [aroma.affymetrix] Questions on extracting probeset summaries
Hi, Henrik, Thanks for the reply! Here is my code: library(aroma.affymetrix) RawName = Project1 RawChipType = HG-U133_Plus_2 ces - doGCRMA(RawName, chipType = RawChipType) data - extractDataFrame(ces, units = NULL, addNames = TRUE) Here is the sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF -8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_GB.UTF-8LC_MESSAGES=en_US .UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION =C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.light_2.2.1 aroma.affymetrix_2.13.0 aroma.core_2.13.0 R.devices_2.12.0 [5] R.filesets_2.6.0R.utils_1.34.0 R.oo_1.18.2 affxparser_1.38.0 [9] R.methodsS3_1.6.2 loaded via a namespace (and not attached): [1] aroma.apd_0.5.0base64enc_0.1-2Cairo_1.5-7digest_0.6.8 DNAcopy_1.40.0 [6] matrixStats_0.13.0 PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0 R.rsp_0.19.7 [11] tools_3.1.1 Here is the traceback() 1: extractDataFrame(ces, units = NULL, addNames = TRUE) I tried several times, but always got a data frame containing 27604 obj. :-( Thanks On Friday, 23 January 2015 01:36:00 UTC+8, Henrik Bengtsson wrote: On Thu, Jan 22, 2015 at 5:44 AM, Qingzhou Zhang zqzne...@gmail.com javascript: wrote: Hi Henrik, I was processing HG-U133_Plus_2 datasets. While extracting probeset summaries(chip effects) as a data frame, I only got 27604 objs * n variables. I was hoping to get a data frame of 54675 objs., which equals the number of units in HG-U133_Plus_2 chip. Am I missing some steps, or processing the wrong CEL files? Hard to say. Can you share your code (from beginning to end) showing what you're doing? Henrik Thanks a lot! -- -- 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 because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-af...@googlegroups.com javascript: To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetr...@googlegroups.com javascript:. For more options, visit https://groups.google.com/d/optout. -- -- 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 because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [aroma.affymetrix] Re: Regarding the copy number states and further processing
Hi guys, here are some late feedback on this discussion: * When talking about copy numbers, it is important to always be very clear and distinguish between whether we talk about normal/germline CNs or tumor CNs. The former take integer CN levels (0, 1, 2, 3, ...), whereas for tumors we very rarely observe pure homogeneous tumor cells, which is why we only measure and observe non-integer CN levels. Hopefully, we observe at least discrete CN levels in tumors, but one should never expect integer levels. * aCGH: a historical term often used as a synonym for total copy numbers. For example, some say aCGH analysis when they really mean total copy-number analysis. aCGH stands for array-CGH, or in full 'array comparative genomic hybridization'. This refers to the older generation two-color/two-channel arrays where a test and a reference sample where labelled with two different dyes and competitively hybridized to the same array and the same probes. I recommend to stop using this term and instead use total copy number, total CN, or TCN (when it's clear). By being explicit about total, you're also explicitly contrasting it to parent-specific CNs (which you can do if you have SNP data). * CNA: Copy-Number Aberration. This term can be applied to both tumor and germline samples. In tumors you expect non-integer CN levels. In germline/normals you expect integer CN levels (0, 1, 2, 3, ...). * CNP: Copy-Number Polymorphism. This term applies to copy-number differences in relationship to a population. This also implies we're talking about germline genomes. In other words, CNPs are also integer CN levels (0, 1, 2, 3, ...). CNPs are used to specify, say, 2% of the Europeans have a 1 copy deletion of length 1.0-1.5 Mb on Chr 3 at 124.5Mb. CNPs is for segment deletions and gains what SNPs are for nucleotide polymorphisms. The term CNP is rare. It is much more common to hear/see CNV. * CNV: Copy-Number Variation. Ideally the word variation refers to polymorphism and therefore the term CNV should be used only to refer to CNPs. I don't know if there is a formal definitions, but I find it unfortunate to see CNV being used when CNA should be used. By my books, CNV only takes integer CN levels (0, 1, 2, 3, ...). The term CNV should never be used to refer to CN levels in tumors. * Calling total CN levels is very hard in tumors, and as the first above point alludes to, it may not even be a well defined problem. For instance, imagine you have a tumor sample with 5% tumor cells and 95% normal cells, and that the those tumors cells all have a deletion on Chr 2. Then, at what point to you consider that sample itself to have a deletion on Chr 2? Are you after he sample/tissue itself, or are you after those 5% tumors cells? What if you have a heterogeneous mix of tumor cells? The more precise you can specify your question the more easy it is for you to decided what approach forward (may) work and what doesn't work. Here work can also be read as make sense. * The first and most important task for almost all segmentation methods is to *segment* the genome, that is, identify at what genomic locations the observed DNA (tumor, normal or a mix) changes in CN level. Together, these location, aka change points, defines how the genome can be partitioned into segments with equal CN levels, such that when we look at a particular segment, we can assume that all genomic locations within that segment has the same underlying genomic composition (e.g. gain, loss, loss in 5% of the cells, etc.). CBS, GLAD, and many other methods, segment the genome this way as a first step. * A common task after having decided on the segments (partitioning of the genome), is to decide on what is going on within each segment. Not all methods does this. For instance, CBS only provides you with the change points. GLAD on the other hand does both the segmentation and then also provides a method for calling. Theoretically, there is nothing preventing you from using the GLAD *calling* algorithm using the segmentation found by CBS. Unfortunately, I don't think it is straightforward to do that in practice; at least you have to coerce one data format into one that GLAD understands. * GLAD does not scale well with the number of loci, because it's computational complexity is ~O(n^2), unless things have changed since. In 2007, I tried to predict GLAD's processing time when we were using the Affymetrix 500K chips and the GenomeWideSNP_5 and GenomeWideSNP_6 were starting to come out. A GWS6 chip would basically take days to segment. See attached PNG for a table. * CBS is much faster as an algorithm. Also, the implementation in the DNAcopy package has been made even faster over time. There was a major speedup back in 2009, cf. http://aroma-project.org/benchmarks/DNAcopy_v1.19.2-speedup/ Over and for now Henrik On Thu, Jan 22, 2015 at 12:42 AM, Chengyu Liu chengyu.liu...@gmail.com wrote: Hi, I have tried this and works good but at the
Re: [aroma.affymetrix] Questions on extracting probeset summaries
On Thu, Jan 22, 2015 at 5:44 AM, Qingzhou Zhang zqznept...@gmail.com wrote: Hi Henrik, I was processing HG-U133_Plus_2 datasets. While extracting probeset summaries(chip effects) as a data frame, I only got 27604 objs * n variables. I was hoping to get a data frame of 54675 objs., which equals the number of units in HG-U133_Plus_2 chip. Am I missing some steps, or processing the wrong CEL files? Hard to say. Can you share your code (from beginning to end) showing what you're doing? Henrik Thanks a lot! -- -- 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 because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. -- -- 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 because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
