Dear Henrik I have sent this offline to Affymetrix DevNet, so you will not find any note.
I have already done this once for the MoGene and RaGene arrays where Affymetrix has deleted one AFFX control in the PGF-files but not in the corresponding annotation files, see: https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-August/029049.html However, this time they have added a few hundred probesets to the annotation file which are not present in the PGF-file, see their README file for the updated HuGene annotation file. BTW, I really hope that Affymetrix (and you) will soon update the annotation files for the SNP arrays to hg19, i.e. human genome build 37. Best regards Christian On Feb 8, 11:09 am, Henrik Bengtsson <[email protected]> wrote: > 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 > > athttp://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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