Re: [aroma.affymetrix] [process and display function in aroma.affymetrix]
On Sat, Sep 20, 2014 at 9:11 PM, jjspring OH sshshoh1...@gmail.com wrote: Thanks! Yes, it seems it is due to old version for manual example, Everything is done when i follow the URL for now and getting display(ae) result (attached file) BTW just checking out for one warning message from plm fitting before getting into alternative splicing part, is it ok to ignore the message ? what exactly does it mean? fit(plmTr, verbose=verbose) Warning message: In fitfcn(y, ...) : Ignoring a unit group when fitting probe-level model, because it has a ridiculously large number of data points: 6515x8 5000x1 See 'models/RmaPlm/skipThreshold' on http://aroma-project.org/settings /Henrik Thanks again, Best Sunghee 2014년 9월 21일 일요일 오전 1시 46분 6초 UTC+9, Henrik Bengtsson 님의 말: How are you setting up the ArrayExplorer? It looks like you're missing to set the color maps. Are you following a particular example (URL?) that could be wrong. Have a look at http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis for an example. /Henrik On Sat, Sep 20, 2014 at 4:03 AM, jjspring OH sshsh...@gmail.com wrote: And also, For process(ae) getting warning messages(pls see below) it seems to be related with next command lines it does not matter? could you please take a closer look at these as well? curent sessionInfo is R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] R.rsp_0.19.3aroma.light_2.0.0 matrixStats_0.10.0 [4] aroma.affymetrix_2.12.8 aroma.core_2.12.8 R.devices_2.11.4 [7] R.filesets_2.6.0R.utils_1.33.7 R.oo_1.18.2 [10] affxparser_1.36.0 R.methodsS3_1.6.1 loaded via a namespace (and not attached): [1] aroma.apd_0.5.0 base64enc_0.1-2 digest_0.6.4DNAcopy_1.38.1 [5] PSCBS_0.43.0R.cache_0.11.0 R.huge_0.8.0tools_3.1.1 process(ae) Loading required package: R.rsp R.rsp v0.19.3 (2014-08-29) successfully loaded. See ?R.rsp for help. Attaching package: ‘R.rsp’ The following object is masked from ‘package:aroma.affymetrix’: getParameter The following objects are masked from ‘package:aroma.core’: getParameters, process, write The following objects are masked from ‘package:R.filesets’: getAttribute, getAttributes, getFile, getFileSize, getHeader, nbrOfLines, setAttribute, setAttributes The following objects are masked from ‘package:R.utils’: parse, parse.default The following objects are masked from ‘package:base’: flush, parse, stop, write The following object is masked _by_ package:aroma.affymetrix: writeCdf The following object is masked _by_ package:R.utils: findFiles 20140920 19:48:32|Color maps: 20140920 19:48:32|Chip type: RaGene-1_0-st-v1,r3 20140920 19:48:40|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ 5_(RaGene-1_0-st-v1),residuals 20140920 19:48:40|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) 20140920 19:48:47|Color maps: 20140920 19:48:47|Chip type: RaGene-1_0-st-v1,r3 20140920 19:48:54|Samples: CS _ 10_(RaGene-1_0-st-v1),residuals, CS _ 12_(RaGene-1_0-st-v1),residuals, CS _ 7_(RaGene-1_0-st-v1),residuals, CS _ 8_(RaGene-1_0-st-v1),residuals, NS _ 1_(RaGene-1_0-st-v1),residuals, NS _ 3_(RaGene-1_0-st-v1),residuals, NS _ 4_(RaGene-1_0-st-v1),residuals, NS _ 5_(RaGene-1_0-st-v1),residuals 20140920 19:48:54|Aliases: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ 7_(RaGene-1_0-st-v1), CS _ 8_(RaGene-1_0-st-v1), NS _ 1_(RaGene-1_0-st-v1), NS _ 3_(RaGene-1_0-st-v1), NS _ 4_(RaGene-1_0-st-v1), NS _ 5_(RaGene-1_0-st-v1) [1] FALSE Warning messages: 1: In fcn(...) : Packages reordered in search path: package:affxparser 2: In parseRepos(sets = repos, where = where, fallback = fallback, : Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ - ‘http://cran.r-project.org’ 3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 4: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases = aliases, : No color maps specified. Nothing to do. 5: In parseRepos(sets = repos, where = where, fallback = fallback,
[aroma.affymetrix] transcript and exon level analysis for detection of alternative splicings
Hi, I would like to compare the results from plmTr and plmEx, estimation of overall expression for transcripts and exon-by-exon estimation, but when i tried to run ExonRmaPlm with mergeGroups = T and F, respectively, i am getting the identical results for following objects including FIRMA scores based on 29170 rows by samples, plmTr - ExonRmaPlm(csN, mergeGroups=TRUE) print(plmTr) plmEx - ExonRmaPlm(csN, mergeGroups=FALSE) print(plmEx) ... firma - FirmaModel(plmEx) fit(firma, verbose=verbose) fs - getFirmaScores(firma) asData - extractDataFrame(fs, addNames=TRUE) fs - getFirmaScores(firma) asData - extractDataFrame(fs, addNames=TRUE) dim(asData) [1] 2917013 Yet, And also, when i ran previously in oligo library, got 213067 probe indices library(oligo) celFiles = list.celfiles( '/Users/sungheeoh/Desktop/SUNGHEE/PROJS/KANG/RAW-CELFILES/',full.name =T) raw = read.celfiles(celFiles) exon_rma = rma(raw,target=probeset) #pre-processing/normalization/log2-scale exon_mat - exprs(exon_rma) dim(exon_mat) head(exon_mat) dim(exon_mat) [1] 213067 8 My questions, first question is how i can get different sets from transcript and exon-by-exon from cell files? and also, just curious, how is it mapped from probe sets (213K) onto transcript/exon level annotation(29K)? And, major interest is to detect differentially alternative splicings for each gene? (we are mostly interested in looking at those genes, e.g. Although a gene is differentially expressed but it is not differentially expressed in AS or vice versa,) how can i extract these information from FIRMA scores? could you pls let me know ? Thanks a lot in advance, Sunghee -- -- 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: transcript and exon level analysis for detection of alternative splicings
And one more question: On the FIRMA scores, what are NA values, though expression levels are not zero? Thanks, Sunghee 2014년 9월 22일 월요일 오전 10시 50분 25초 UTC+9, jjspring OH 님의 말: Hi, I would like to compare the results from plmTr and plmEx, estimation of overall expression for transcripts and exon-by-exon estimation, but when i tried to run ExonRmaPlm with mergeGroups = T and F, respectively, i am getting the identical results for following objects including FIRMA scores based on 29170 rows by samples, plmTr - ExonRmaPlm(csN, mergeGroups=TRUE) print(plmTr) plmEx - ExonRmaPlm(csN, mergeGroups=FALSE) print(plmEx) ... firma - FirmaModel(plmEx) fit(firma, verbose=verbose) fs - getFirmaScores(firma) asData - extractDataFrame(fs, addNames=TRUE) fs - getFirmaScores(firma) asData - extractDataFrame(fs, addNames=TRUE) dim(asData) [1] 2917013 Yet, And also, when i ran previously in oligo library, got 213067 probe indices library(oligo) celFiles = list.celfiles( '/Users/sungheeoh/Desktop/SUNGHEE/PROJS/KANG/RAW-CELFILES/',full.name =T) raw = read.celfiles(celFiles) exon_rma = rma(raw,target=probeset) #pre-processing/normalization/log2-scale exon_mat - exprs(exon_rma) dim(exon_mat) head(exon_mat) dim(exon_mat) [1] 213067 8 My questions, first question is how i can get different sets from transcript and exon-by-exon from cell files? and also, just curious, how is it mapped from probe sets (213K) onto transcript/exon level annotation(29K)? And, major interest is to detect differentially alternative splicings for each gene? (we are mostly interested in looking at those genes, e.g. Although a gene is differentially expressed but it is not differentially expressed in AS or vice versa,) how can i extract these information from FIRMA scores? could you pls let me know ? Thanks a lot in advance, Sunghee -- -- 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.
