Glad to hear it working. I will investigate the problem related to the iter-plier usage. Cheers Raffaele Il 14/06/2010 14:52, Steve Taylor ha scritto: > Hi, > >> after Steve, sent me the sessionInfo() results, it came out that he was >> using onechannelGUI from Bioconductor release 2.5. oneChannelGUI >> released with Bioconductor 2.6 now allows to handle both normal gene >> arrays and 96 format gene arrays. For this reason in the library files >> that are associated to oneChannelGUI there are two different types of >> Gene array library files: >> HuGene-1_0-st-v1 and HuGene-1_1-st-v1 >> So I told Steve to upgrade the oneChannelGUI installation and the >> problem will be solved. > > Thanks for your advice. > > I upgraded to the latest version of R/OneChannelGUI and it is > basically working, though there seem to be a bug using Iter-plier. > > Here is the output when loading in the data using RMA-Sketch >> > Gene level probe sets summary started > Read 12 cel files from: target79e2a9e3 > Opening clf file: HuGene-1_0-st-v1.r4.clf > Opening pgf file: HuGene-1_0-st-v1.r4.pgf > Expecting 1 iteration. > Doing iteration: 1 > Opening clf file: HuGene-1_0-st-v1.r4.clf > Opening pgf file: HuGene-1_0-st-v1.r4.pgf > Loading 33297 probesets and 804955 probes. > Reading 12 cel files............Done. > Processing Probesets......................Done. > Flushing output reporters. Finalizing output. > Done. > Cleaning up. > Done. > Run took approximately: 0.96 minute. > > But if I use Iter-plier > > Gene level probe sets summary started > Read 12 cel files from: target1d4ed43b > Opening bgp file: > terminate called after throwing an instance of 'std::ios_base::failure' > what(): basic_filebuf::underflow error reading the file > > Gene level probe sets summary ended > Error in as.matrix(my.exons) : > no function to return from, jumping to top level > In addition: Warning messages: > 1: In file(file, "rt") : only first element of 'description' argument > used > 2: In file(file, "rt") : only first element of 'description' argument > used > > Also, is there anyway to change the font size in the QC steps (e.g. > PCA plot/Dendrogram display)? > > Thanks again, > > Steve > > >> Cheers >> Raffaele >> >> >> >> Il 09/06/2010 21:23, cstrato ha scritto: >>> Dear Raffaele, >>> >>> I do not think that this is an error from APT tools unable to read >>> some of the CEL files. >>> >>> The output: >>> Wrong number of cells: Expecting: 1178100 and 2A.CEL has: 1102500 >>> suggests that the PGF-file for HuGene-1_1-st-v1 was used and not the >>> PGF-file for HuGene-1_0-st-v1: >>> >>> HuGene-1_0-st-v1 has a size of 1050 x 1050 = 1102500 >>> HuGene-1_1-st-v1 has a size of 1190 x 990 = 1178100 >>> >>> Thus for 2A.CEL APT seems to require the PGF-file for HuGene- 1_0-st-v1. >>> >>> Best regards >>> Christian >>> _._._._._._._._._._._._._._._._._._ >>> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a >>> V.i.e.n.n.a A.u.s.t.r.i.a >>> e.m.a.i.l: cstrato at aon.at >>> _._._._._._._._._._._._._._._._._._ >>> >>> >>> On 6/9/10 2:54 PM, rcaloger wrote: >>>> Il 09/06/2010 12:00, bioconductor-request at stat.math.ethz.ch ha >>>> scritto: >>>>> Steve Taylor<stephen.taylor at="" imm.ox.ac.uk=""> >>>> Dear Steve, >>>> there is some problem with the cel files you are using as indicated by >>>> the error: >>>> >>>> Wrong number of cells: Expecting: 1178100 and 1A.CEL has: 1102500 >>>> Wrong number of cells: Expecting: 1178100 and 2A.CEL has: 1102500 >>>> >>>> This is an error from APT tools which are unable to read some of your >>>> CEL file. >>>> Furthermore, you must have an error in the target file used to load >>>> the >>>> data set, since >>>> the software try to read CEL file 3.CEL >>>> >>>> FATAL ERROR: Can't read file: 3.CEL >>>> >>>> but this is not present in the list of arrays you have indicated in >>>> the >>>> mail. >>>> >>>> To help you in solving your problem I need to know which are the >>>> arrays >>>> under analysis: >>>> human, mouse, rat >>>> gene, exon arrays >>>> >>>> To have an idea of the installation please write in the main R window: >>>> sessionInfo() >>>> affylmGUIenvironment$libDirLocation >>>> affylmGUIenvironment$aptDir >>>> >>>> and send the output to me. >>>> Cheers >>>> Raffaele >>>> >>>> >>>> >>>>> Hi, >>>> >>>>> I am trying use oneChannelGUI to analyse some Affymetrix 1.0 ST >>>>> arrays >>>>> but I can't read in the data. I have two questions: >>>> >>>>> 1) Why is this not working in OneChannelGUI? >>>>> 2) If I can't get this to work, what are the best alternatives to >>>>> read >>>>> and normalise this data (to be> >>>>> subsequently analysed by LIMMA)? >>>> >>>>> 1A.CEL >>>>> 1B.CEL >>>>> 2A.CEL >>>>> 2B.CEL >>>>> T10.CEL >>>>> T11.CEL >>>>> T12.CEL >>>>> T3.CEL >>>>> T4.CEL >>>>> T5.CEL >>>>> T6.CEL >>>>> T7.CEL >>>>> T8.CEL >>>>> T9.CEL >>>>> Using OneChannelGUI, when I try and read in the CEL files >>>>> using>rma-sketch or iter-plier I get >>>> >>>>> Error >>>>> in>read.table(paste(tempOut,"/",content.outDir[tempOut1],sep=""),: >>>>> no lines available in input >>>> >>>>> and then various other errors in the Tk window. In my terminal >>>>> window>I get: >>>> >>>>> Gene level probe sets summary started >>>>> Read 12 cel files from: target327b23c6 >>>>> Wrong number of cells: Expecting: 1178100 and 1A.CEL has: 1102500 >>>>> Wrong number of cells: Expecting: 1178100 and 2A.CEL has: 1102500 >>>> >>>>> FATAL ERROR: Can't read file: 3.CEL >>> >> >> > -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze Cliniche e Biologiche c/o Az. Ospedaliera S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705417 Lab. ++39 0116705408 Fax ++39 0119038639 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it Info: http://publicationslist.org/raffaele.calogero

Hi Steve, many thanks for the bug report. The bug in the usage of iter-plier summarization for gene arrays is fixed in oneChannelGUI 1.14.4, which should be available in a 24 hours on the bioconductor web Cheer Raffaele Il 14/06/2010 14:52, Steve Taylor ha scritto: > Hi, > >> after Steve, sent me the sessionInfo() results, it came out that he was >> using onechannelGUI from Bioconductor release 2.5. oneChannelGUI >> released with Bioconductor 2.6 now allows to handle both normal gene >> arrays and 96 format gene arrays. For this reason in the library files >> that are associated to oneChannelGUI there are two different types of >> Gene array library files: >> HuGene-1_0-st-v1 and HuGene-1_1-st-v1 >> So I told Steve to upgrade the oneChannelGUI installation and the >> problem will be solved. > > Thanks for your advice. > > I upgraded to the latest version of R/OneChannelGUI and it is > basically working, though there seem to be a bug using Iter-plier. > > Here is the output when loading in the data using RMA-Sketch >> > Gene level probe sets summary started > Read 12 cel files from: target79e2a9e3 > Opening clf file: HuGene-1_0-st-v1.r4.clf > Opening pgf file: HuGene-1_0-st-v1.r4.pgf > Expecting 1 iteration. > Doing iteration: 1 > Opening clf file: HuGene-1_0-st-v1.r4.clf > Opening pgf file: HuGene-1_0-st-v1.r4.pgf > Loading 33297 probesets and 804955 probes. > Reading 12 cel files............Done. > Processing Probesets......................Done. > Flushing output reporters. Finalizing output. > Done. > Cleaning up. > Done. > Run took approximately: 0.96 minute. > > But if I use Iter-plier > > Gene level probe sets summary started > Read 12 cel files from: target1d4ed43b > Opening bgp file: > terminate called after throwing an instance of 'std::ios_base::failure' > what(): basic_filebuf::underflow error reading the file > > Gene level probe sets summary ended > Error in as.matrix(my.exons) : > no function to return from, jumping to top level > In addition: Warning messages: > 1: In file(file, "rt") : only first element of 'description' argument > used > 2: In file(file, "rt") : only first element of 'description' argument > used > > Also, is there anyway to change the font size in the QC steps (e.g. > PCA plot/Dendrogram display)? > > Thanks again, > > Steve > > >> Cheers >> Raffaele >> >> >> >> Il 09/06/2010 21:23, cstrato ha scritto: >>> Dear Raffaele, >>> >>> I do not think that this is an error from APT tools unable to read >>> some of the CEL files. >>> >>> The output: >>> Wrong number of cells: Expecting: 1178100 and 2A.CEL has: 1102500 >>> suggests that the PGF-file for HuGene-1_1-st-v1 was used and not the >>> PGF-file for HuGene-1_0-st-v1: >>> >>> HuGene-1_0-st-v1 has a size of 1050 x 1050 = 1102500 >>> HuGene-1_1-st-v1 has a size of 1190 x 990 = 1178100 >>> >>> Thus for 2A.CEL APT seems to require the PGF-file for HuGene- 1_0-st-v1. >>> >>> Best regards >>> Christian >>> _._._._._._._._._._._._._._._._._._ >>> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a >>> V.i.e.n.n.a A.u.s.t.r.i.a >>> e.m.a.i.l: cstrato at aon.at >>> _._._._._._._._._._._._._._._._._._ >>> >>> >>> On 6/9/10 2:54 PM, rcaloger wrote: >>>> Il 09/06/2010 12:00, bioconductor-request at stat.math.ethz.ch ha >>>> scritto: >>>>> Steve Taylor<stephen.taylor at="" imm.ox.ac.uk=""> >>>> Dear Steve, >>>> there is some problem with the cel files you are using as indicated by >>>> the error: >>>> >>>> Wrong number of cells: Expecting: 1178100 and 1A.CEL has: 1102500 >>>> Wrong number of cells: Expecting: 1178100 and 2A.CEL has: 1102500 >>>> >>>> This is an error from APT tools which are unable to read some of your >>>> CEL file. >>>> Furthermore, you must have an error in the target file used to load >>>> the >>>> data set, since >>>> the software try to read CEL file 3.CEL >>>> >>>> FATAL ERROR: Can't read file: 3.CEL >>>> >>>> but this is not present in the list of arrays you have indicated in >>>> the >>>> mail. >>>> >>>> To help you in solving your problem I need to know which are the >>>> arrays >>>> under analysis: >>>> human, mouse, rat >>>> gene, exon arrays >>>> >>>> To have an idea of the installation please write in the main R window: >>>> sessionInfo() >>>> affylmGUIenvironment$libDirLocation >>>> affylmGUIenvironment$aptDir >>>> >>>> and send the output to me. >>>> Cheers >>>> Raffaele >>>> >>>> >>>> >>>>> Hi, >>>> >>>>> I am trying use oneChannelGUI to analyse some Affymetrix 1.0 ST >>>>> arrays >>>>> but I can't read in the data. I have two questions: >>>> >>>>> 1) Why is this not working in OneChannelGUI? >>>>> 2) If I can't get this to work, what are the best alternatives to >>>>> read >>>>> and normalise this data (to be> >>>>> subsequently analysed by LIMMA)? >>>> >>>>> 1A.CEL >>>>> 1B.CEL >>>>> 2A.CEL >>>>> 2B.CEL >>>>> T10.CEL >>>>> T11.CEL >>>>> T12.CEL >>>>> T3.CEL >>>>> T4.CEL >>>>> T5.CEL >>>>> T6.CEL >>>>> T7.CEL >>>>> T8.CEL >>>>> T9.CEL >>>>> Using OneChannelGUI, when I try and read in the CEL files >>>>> using>rma-sketch or iter-plier I get >>>> >>>>> Error >>>>> in>read.table(paste(tempOut,"/",content.outDir[tempOut1],sep=""),: >>>>> no lines available in input >>>> >>>>> and then various other errors in the Tk window. In my terminal >>>>> window>I get: >>>> >>>>> Gene level probe sets summary started >>>>> Read 12 cel files from: target327b23c6 >>>>> Wrong number of cells: Expecting: 1178100 and 1A.CEL has: 1102500 >>>>> Wrong number of cells: Expecting: 1178100 and 2A.CEL has: 1102500 >>>> >>>>> FATAL ERROR: Can't read file: 3.CEL >>> >> >> > -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze Cliniche e Biologiche c/o Az. Ospedaliera S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705417 Lab. ++39 0116705408 Fax ++39 0119038639 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it Info: http://publicationslist.org/raffaele.calogero