Hi. On Mon, Feb 1, 2010 at 9:02 AM, cstratowa <[email protected]> wrote: > Dear Branko, > > I have just seen your comment that you have an issue with XPS, which > is my BioC package. However, you have never contacted me at > <[email protected]> nor have sent a mail to the BioC mailing list. I > would really appreciate that you contact me first before making such a > statement. > > Regarding your problem with HuGene-1_0-st-v1.na30.hg19.probeset._csv, > (which could be the reason of your problem with xps), Affymetrix had > included probesets in this annotation file which were not included in > the corresponding *.PGF file. For this reason I have contacted > Affymetrix DevNet and asked them to remove the extra probesets, which > they kindly did resulting in file HuGene-1_0-st- > v1.na30.1.hg19.probeset._csv.
Thanks for this note/update. Did you send this offline to Affymetrix or did you use their Affymetrix Scientific Community Forums [https://www.affymetrix.com/community/forums/index.jspa]? I could find it in the latter, but there are quite a few forums too. Cheers, Henrik > > Best regards > Christian > > On Jan 28, 4:58 pm, branko <[email protected]> wrote: >> Hi all, >> >> First to thank you Mark , Henrik for nice tool and also all others >> for informative mailing list. >> This is my first email so hopefully not so many dummy questions. >> >> I found this thread as it is linked to my first 2 questions: >> Month ago I did some basic analysis with 300 chips where your tool >> got very handy. And I'm starting again to analyze things ... >> (Btw. I found about Aroma on BioC list as I had issue with XPS >> package that I couldn’t resolve . I would like to have them both >> working so Xps will come on board eventually.) >> >> Now regarding this tread. >> 1) When I compared HuGene-1_0-st-v1.na30.hg19.probeset._csv. with >> the Aroma CDF file there are >> 33257 PSets in csv while Aroma has 33252 so 4 different. So >> maybe the CDF update is needed in Aroma? >> I also just saw some more recent update on Affymetrix to “na30.1” >> and I see I have used “na30” csv file. >> >> Following seems weird , many ProbeSets have no gene symbol >> annotation in “main“ category : >> >> tr <- read.csv ( "HuGene-1_0-st-v1.na30.hg19.transcript.csv" , >> stringsAsFactors =F ,comment.char="#") >> >> sum(tr$gene_assignment=="---" & tr$category=="main") #6711 >> sum(tr$unigene=="---" & tr$category=="main") #7376 >> sum(tr$swissprot=="---" & tr$category=="main") # 8021 >> >> Affy 33257 Probesets are classified as: >> TYPE TOTAL >> control->affx 57 >> control->bgp->antigenomic 45 >> main 28829 >> normgene->exon 1195 >> normgene->intron 2904 >> rescue->FLmRNA->unmapped 227 >> >> Do you maybe know why are there so many e.g above 6711 without >> gene_assignment ? >> >> 2) One more related to 1st Q : How to run normalization only on >> ProbeSet classified as “main” ? ( Affymetrix csv file says this >> class has 28829 >> Psets in main class) Idea is of course to minimize >> normalization bias of non-main class Psets. >> >> 3) Few questions regarding Quality checks and basic data >> manipulations in Aroma: >> I would like to give meaningful labels to the Arrays in the e.g. >> box-plots (instead of CEL file names, as said i have 300) . >> How can I do that? >> Also how can I sort them ? >> I ask this silly questions because Using R commands like str() >> doesn’t show me the >> object fields etc. so I can’t use standard R matrix commands, >> also help (“some Aroma command” ) doesn’t show enough information. >> Sometimes it gives empty help page. >> I could not find pdf manual in Aroma installed libraries nor in >> the Google group. I see only html file showing me all the functions & >> classes. >> Is there easier way to look for functions than main html pages ? >> Code of functions are not visible by just typing func.name() , I >> guess I can always get source code and search but there is likely easy >> way to do it. >> >> It is visible that Aroma uses different classes than >> BioConductor. I assume there is a good reason for that, but maybe you >> can give some link with explanation? >> >> Oh and thank you for putting clean instructions for basic >> preprocessing steps to get Expression matrix out for further >> analysis. >> >> One example of my attempt to searching things : >> cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf) >> print(cs) >> str(cs) >> #Classes 'AffymetrixCelSet', 'AffymetrixFileSet', >> 'AromaPlatformInterface', 'AromaMicroarrayDataSet', >> 'GenericDataFileSet', 'FullNameInterface', 'Object' atomic [1:1] NA >> …. >> ?classname put me on some track. >> >> So I looked a bit and I saw GenericDataFileSet class provides >> function >> getFullNames() and it does give me the my CEL filenames (btw. >> help on ?getFullNames gives me no help .) >> setNames() point to basic library… but before going deeper and >> making some mess I hope you >> can give me answer on above questions or some links ? >> >> 4) Last one , regarding QC issue with plotting … SO when doing Array >> (pseudo) image plots my RGui in windows complains e.g.: >> >> If I do: cf <- getFile (cs, 1) >> plotImage(cf, transform=list(log2), palette=rainbow >> (256)) >> >> #Loading required package: EBImage >> #Loading required package: abind >> …. >> >> I get “Runtime error!” message from Visual C++ and I have to >> click 2 times “ok” and then I get the picture… >> Here is the link to the error msg:: >> http://www.4shared.com/file/209798878/f5a3f82e/Aromaplotimageerror.html >> >> SO you can imagine I’m not enthusiastic of clicking twice for 300 >> arrays and then again for several type of plots. >> Any idea where is the issue ? (I guess something with EBImage >> dependency make issue ) >> Below is my session info . >> >> Hope you can help . >> >> Best regards, >> >> Branko >> >> -------------------------- >> Branislav Misovic, >> Department of Toxicogenetics >> Leiden University Medical Center >> PO.box 9600, Building2,Room:T3-11 >> 2300 RC Leiden >> The Netherlands >> Phone: +31 71 526 9636 >> Mob: 0653135855 >> E-mail: [email protected] >> >> > sessionInfo() >> R version 2.10.0 (2009-10-26) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United >> Kingdom.1252 >> [3] LC_MONETARY=English_United Kingdom.1252 >> LC_NUMERIC=C >> [5] LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods >> base >> >> other attached packages: >> [1] abind_1.1-0 aroma.affymetrix_1.3.4 >> aroma.apd_0.1.7 >> [4] affxparser_1.18.0 R.huge_0.2.0 >> aroma.core_1.3.4 >> [7] aroma.light_1.15.1 matrixStats_0.1.8 >> R.rsp_0.3.6 >> [10] R.filesets_0.6.5 digest_0.4.1 >> R.cache_0.2.0 >> [13] R.utils_1.2.4 R.oo_1.6.6 >> EBImage_3.2.0 >> [16] R.methodsS3_1.0.3 >> >> loaded via a namespace (and not attached): >> [1] tools_2.10.0 >> >> -------------------------- >> Branislav Misovic, >> Department of Toxicogenetics >> Leiden University Medical Center >> PO.box 9600, Building2,Room:T3-11 >> 2300 RC Leiden >> The Netherlands >> Phone: +31 71 526 9636 >> Mob: 0653135855 >> E-mail: [email protected] > > -- > 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. > To post to this group, send email to [email protected] > To unsubscribe from this group, send email to > [email protected] > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en -- 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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