Hello, there, I am using beadarray package developed by Mark Dunning for Illumina expression arrays. Have 2 question regarding to this package: 1. There is annotation file Illumina_HumanWG-6_V2_0_R1_11223189_A.bgx in the data set I downloaded form GEO. Unfortunately readIllumina() didn't recognize this file, instead it asked for "Humanv3 Humanv2 Humanv1 Mousev2 Mousev1 Mousev1p1 Ratv1". Illumina has expression arrays: - HumanHT-12 Expression BeadChip - HumanWG-6 v3 Expression - HumanRef-8 v3 Expression BeadChip - MouseWG-6 v2 Expression - MouseRef-8 v2 Expression BeadChip - RatRef-12 Expression BeadChip So where I can get these "Humanvs, Humanv2..." files? and which annotation is for which array? 2. There are tif files for each sample in data set. But file extension is .tif not_Grn.tif. I got following errors when reading data. What's wrong? ---------------------------------------------------------------------- -------------------------------------------------- > d<-readIllumina(useImages=T, tiffExtGrn=".tif") Found 0 arrays Error in seq.default(1, length(tmp), by = 3) : wrong sign in 'by' argument In addition: Warning message: In readIllumina(useImages = T, tiffExtGrn = ".tif") : No annotation package was specified. Need to use SetAnnotation later ---------------------------------------------------------------------- --------------------------------------------------- Thank you very much. yezhou [[alternative HTML version deleted]]

Hello, Thanks for your questions. The first relates to a new piece of functionality added to beadarray that has not been explained in depth yet. 1. The names Humanv3, Humanv2, Humanv1 etc are used to identify the type of chip being read in. This is so we know the ids of the control probes on the chip (which change between versions and organisms). The information about the control probes is stored with the package so there is no need to download extra information. It is completely separate to the annotation Illumina provides and the Bioconductor packages. The naming convention we used is chosen to match the names of the annotation packages available from Bioconductor. For example if you have a HumanWG-6 v3 Expression array you would specify annoPkg="Humanv3" when you load data with readIllumina and then use the illuminaHumanv3BeadID.db annotation package later on. 2. Can you list the files that are in the working directory where you are trying to read from? Each sample should have a _Grn.tif and .txt file for a bead-level analysis Regards, Mark PS posting the result of running the command sessionInfo() is also useful so we know what version of packages you are running. On Thu, 2008-11-13 at 21:02 -0500, Fu Sheng wrote: > Hello, there, > > I am using beadarray package developed by Mark Dunning for Illumina > expression arrays. Have 2 question regarding to this package: > > 1. There is annotation file Illumina_HumanWG- 6_V2_0_R1_11223189_A.bgx in the > data set I downloaded form GEO. Unfortunately readIllumina() didn't > recognize this file, instead it asked for "Humanv3 Humanv2 Humanv1 > Mousev2 Mousev1 Mousev1p1 Ratv1". Illumina has expression arrays: > > - HumanHT-12 Expression BeadChip > - HumanWG-6 v3 Expression > - HumanRef-8 v3 Expression BeadChip > - MouseWG-6 v2 Expression > - MouseRef-8 v2 Expression BeadChip > - RatRef-12 Expression BeadChip > > So where I can get these "Humanvs, Humanv2..." files? and which annotation > is for which array? > > 2. There are tif files for each sample in data set. But file extension is > .tif not_Grn.tif. I got following errors when reading data. What's wrong? > > -------------------------------------------------------------------- ---------------------------------------------------- > > d<-readIllumina(useImages=T, tiffExtGrn=".tif") > Found 0 arrays > Error in seq.default(1, length(tmp), by = 3) : > wrong sign in 'by' argument > In addition: Warning message: > In readIllumina(useImages = T, tiffExtGrn = ".tif") : > No annotation package was specified. Need to use SetAnnotation later > -------------------------------------------------------------------- ----------------------------------------------------- > > Thank you very much. > > yezhou > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hello, Sorry for the delay in replying. So it seems there is a bug in readIllumina when reading GEO data. In short, we assumed that there are 8 characters before the .tif extension (as happens with data produced by the Illumina scanner). However, as these files come from GEO their format is slightly different. It will take a while to fix, but in the meantime you will be able to read these data using the command. d <- readIllumina(useImages=FALSE) This will use the intensities that are already stored in the .txt files which have already been background corrected. For convenience I often use these values anyway as I found Illumina's background correction to be adequate. Hope this helps, Mark -----Original Message----- From: Fu Sheng [mailto:fusheng66@gmail.com] Sent: Fri 14/11/2008 23:32 To: Mark Dunning Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] beadarray package question > > 2. Can you list the files that are in the working directory where you > are trying to read from? Each sample should have a _Grn.tif and .txt > file for a bead-level analysis > > Hello, Mark, Thank you very much for your quick response. I was thinking readIllumina would recognize these .tif files by changing tiffExtGrn parameter. Here is the list of files in working directory: GSM278088.tif GSM290551.tif GSM296419.tif GSM278088.txt GSM290551.txt GSM296419.txt GSM290549.tif GSM290552.tif Illumina_HumanWG- 6_V2_0_R1_11223189_A.bgx GSM290549.txt GSM290552.txt Rplots.pdf GSM290550.tif GSM296418.tif GSM290550.txt GSM296418.txt Here is error message: > d<-readIllumina(annoPkg="Humanv2", tiffExtGrn=".tif", imageManipulation="none", backgroundMethod="none") Found 0 arrays Error in seq.default(1, length(tmp), by = 3) : wrong sign in 'by' argument > traceback() 4: stop("wrong sign in 'by' argument") 3: seq.default(1, length(tmp), by = 3) 2: seq(1, length(tmp), by = 3) 1: readIllumina(annoPkg = "Humanv2", tiffExtGrn = ".tif", imageManipulation = "none", backgroundMethod = "none") > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] beadarray_1.10.0 sma_0.5.15 hwriter_0.93 [4] geneplotter_1.20.0 annotate_1.20.0 xtable_1.5-4 [7] AnnotationDbi_1.4.0 lattice_0.17-15 Biobase_2.2.0 [10] limma_2.16.2 loaded via a namespace (and not attached): [1] DBI_0.2-4 grid_2.8.0 KernSmooth_2.22-22 RColorBrewer_1.0-2 [5] RSQLite_0.7-1 Thank you very much. Have a great weekend! Yezhou This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. [[alternative HTML version deleted]]