On Mon, Nov 19, 2012 at 8:53 PM, Raj Patrao <rlpat...@gmail.com> wrote: > Hentrik, > > I did delete all the files created and re-ran. I deleted complete folder > structure below , as these files are created automatically . > > probeData > GSE4757,GRBC > GSE4757,OBC
Are you saying things work now? > > > Also, I dont know on what basis these datasets are getting created (these > are getting created in the process step), and if the OBC, GRBC annotations > are same for all sets. In each *sequential* step of the pipeline, Aroma adds one or more tags to the data sets names, cf. http://aroma-project.org/node/77 In the case, probeData/GSE4757,OBC/ (optical bg correction) is first created, and then probeData/GSE4757,GRBC/ (gcRMA bg correction) which is based on the former. These two are created by GcRmaBackgroundCorrection. They are not the same. [DETAILS: This case is an outlier on how tags are appended in each step by the Aroma framework; if followed the two data sets should be 'GSE4757,OBC' and 'GSE4757,OBC,GRBC' to indicate that that the latter was created from the former. However, back in time we made an active decision to collapse 'OBC,GRBC' into 'GRBC' to keep names short. Maybe not the best decision looking back.] > As shown in my script : > > for each of the series { > Untar it in a work dir > Gunzip all celfiles > set up cdf > set up cel file set > run background correction <- here the probeData folder gets created > > } > > > I intend to process large number of series in a automated way, so I am > trying these options. Not sure what your question is, but yes, the above approach should work. As long as you follow the standard examples (and don't do your own hacks), the Aroma Framework will make sure that each generated output set (set of files) has a unique file path which reflects what processing has been done and will not clash with other data sets/pipelines. Two analysis pipelines will only generated identical file paths if they are doing the same analysis. /Henrik > > Thanks, > Rajesh. > > On Saturday, November 3, 2012 3:24:39 PM UTC+5:30, Raj Patrao wrote: >> >> Hello All, >> >> I am getting the following error when doing process in aroma: >> >> > csB <- process(bc,verbose=TRUE); >> Background correcting data set... >> Computing probe affinities (independent of data)... >> [2012-11-03 15:10:02] Exception: Failed to identify CDF unit with unit >> name '1': annotationData/chipTypes/HG-U133_Plus_2/u133plus2gb_probe_tab >> >> at #09. getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, >> verbose = verbose) >> - getProbeSequenceData.AffymetrixCdfFile() is in environment >> 'aroma.affymetrix' >> >> at #08. getProbeSequenceData(this, safe = safe, verbose = verbose) >> - getProbeSequenceData() is in environment 'aroma.affymetrix' >> >> at #07. computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., >> verbose = less(verbose)) >> - computeAffinities.AffymetrixCdfFile() is in environment >> 'aroma.affymetrix' >> >> at #06. computeAffinities(cdf, paths = probePath, ..., verbose = >> less(verbose)) >> - computeAffinities() is in environment 'aroma.affymetrix' >> >> at #05. bgAdjustGcrma.AffymetrixCelSet(structure(NA, .env = >> <environment>, class = c("AffymetrixCelSet", >> "AffymetrixFileSet", "AromaPlatformInterface", >> "AromaMicroarrayDataSet", >> "GenericDataFileSet", "FullNameInterface", "Object")), path = >> "probeData/GSE4757,GRBC/HG-U133_Plus_2", >> verbose = structure(TRUE, .env = <environment>, class = >> c("Verbose", >> "Object")), overwrite = FALSE, subsetToUpdate = NULL, >> typesToUpdate = "pm", >> indicesNegativeControl = NULL, affinities = NULL, type = >> "fullmodel", >> opticalAdjust = TRUE, gsbAdjust = TRUE, gsbParameters = >> NULL, >> .deprecated = FALSE) >> - bgAdjustGcrma.AffymetrixCelSet() is in environment >> 'aroma.affymetrix' >> >> at #04. bgAdjustGcrma(structure(NA, .env = <environment>, class = >> c("AffymetrixCelSet", >> "AffymetrixFileSet", "AromaPlatformInterface", >> "AromaMicroarrayDataSet", >> "GenericDataFileSet", "FullNameInterface", "Object")), path = >> "probeData/GSE4757,GRBC/HG-U133_Plus_2", >> verbose = structure(TRUE, .env = <environment>, class = >> c("Verbose", >> "Object")), overwrite = FALSE, subsetToUpdate = NULL, >> typesToUpdate = "pm", >> indicesNegativeControl = NULL, affinities = NULL, type = >> "fullmodel", >> opticalAdjust = TRUE, gsbAdjust = TRUE, gsbParameters = >> NULL, >> .deprecated = FALSE) >> - bgAdjustGcrma() is in environment 'aroma.affymetrix' >> >> at #03. do.call("bgAdjustGcrma", args = args) >> - do.call() is in environment 'base' >> >> at #02. process.GcRmaBackgroundCorrection(bc, verbose = TRUE) >> - process.GcRmaBackgroundCorrection() is in environment >> 'aroma.affymetrix' >> >> at #01. process(bc, verbose = TRUE) >> - process() is in environment 'aroma.core' >> >> Error: >> Computing probe affinities (independent of data)...done >> Background correcting data set...done >> >> >> >> Here is my directory structure : >> >> >annotationData >> >> >> --------> annotationData\chipTypes\HG-U133_Plus_2 >> >> 11/03/2012 03:09 PM <DIR> . >> 11/03/2012 03:09 PM <DIR> .. >> 10/19/2012 10:49 AM 99,044,850 HG-U133_Plus_2 - ascii.cdf >> 10/26/2012 09:49 PM 26,251,783 HG-U133_Plus_2.cdf >> 10/29/2012 10:21 AM 15,952,085 Hs133P_Hs_REFSEQ.cdf >> 07/14/2005 12:23 AM 23,991,168 u133plus2gb_probe_tab >> >> --------> rawData\GSE4757\HG-U133_Plus_2 >> >> 10/26/2012 09:18 PM <DIR> . >> 10/26/2012 09:18 PM <DIR> .. >> 10/26/2012 09:17 PM 13,555,389 GSM107522.cel >> 10/26/2012 09:17 PM 13,556,785 GSM107523.cel >> 10/26/2012 09:17 PM 13,560,384 GSM107524.cel >> 10/26/2012 09:17 PM 13,556,716 GSM107525.cel >> 10/26/2012 09:17 PM 13,552,046 GSM107526.cel >> 10/26/2012 09:17 PM 13,552,689 GSM107527.cel >> 10/26/2012 09:17 PM 13,553,222 GSM107528.cel >> 10/26/2012 09:17 PM 13,552,445 GSM107529.cel >> 10/26/2012 09:17 PM 13,551,059 GSM107530.cel >> 10/26/2012 09:17 PM 13,550,482 GSM107531.cel >> 10/26/2012 09:17 PM 13,550,367 GSM107532.cel >> 10/26/2012 09:17 PM 13,550,546 GSM107533.cel >> 10/26/2012 09:17 PM 13,551,111 GSM107534.cel >> 10/26/2012 09:17 PM 13,551,023 GSM107535.cel >> 10/26/2012 09:17 PM 13,551,624 GSM107536.cel >> 10/26/2012 09:17 PM 13,550,386 GSM107537.cel >> 10/26/2012 09:17 PM 13,552,402 GSM107538.cel >> 10/26/2012 09:17 PM 13,552,977 GSM107539.cel >> 10/26/2012 09:18 PM 13,553,854 GSM107540.cel >> 10/26/2012 09:18 PM 13,553,795 GSM107541.cel >> >> I took the probe tab file from >> http://masker.nci.nih.gov/ev/U133Plus2gb_probe_tab.gz >> >> Please let me know what is wrong and how to proceed. >> >> Thanks, >> Raj >> >> >> >> > -- > 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/ -- 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/
