Hi Alberto, the spot types file is described in detail in section 4.8 of the limma user's guide. And as the first sentence there says, it is optional, so you may as well skip this step -- I haven't used it myself for some time. Cheers, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland From: Alberto Goldoni <alberto.goldoni1975 at="" gmail.com=""> To: axel.klenk at actelion.com Cc: BioC <bioconductor at="" stat.math.ethz.ch="">, bioconductor-bounces at stat.math.ethz.ch Date: 02.09.2010 18:45 Subject: Re: [BioC] help with Agilent microarrays Ok axel, i'll try with limma+vsn but i'm not able to use: spottypes <- readSpotTypes() what kind of txt file i have to use? best regards 2010/9/2 <axel.klenk at="" actelion.com="">: > Hi Alberto, > > at least that's what we do (limma + vsn, actually) and we're happy with > it. > > From a brief glance at the vignette, that is also what Agi4x44KPreProcess > does under the hood but tailored towards one-color 4x44K exclusively, so > just using limma may be a little less convenient but certainly the same > quality. > > BTW, for convenient QC you should have a look at arrayQualityMetrics. > > Cheers, > > - axel > > > Axel Klenk > Research Informatician > Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / > Switzerland > > > > > From: > Alberto Goldoni <alberto.goldoni1975 at="" gmail.com=""> > To: > axel.klenk at actelion.com > Cc: > BioC <bioconductor at="" stat.math.ethz.ch="">, > bioconductor-bounces at stat.math.ethz.ch > Date: > 02.09.2010 16:48 > Subject: > Re: [BioC] help with Agilent microarrays > > > > Thanks Axel, > so you tell me that is better to use limma package to analyse 2 color > agilent? > > 2010/9/2 <axel.klenk at="" actelion.com="">: >> Hi Alberto, >> >> hmmm, has this ever worked before? >> >> AFAIK package Agi4x44KPreProcess supports one-color arrays only. At > least >> we're not using it for exactly that reason. >> >> See: >> > http://article.gmane.org/gmane.science.biology.informatics.conductor/2 1694/match=agi4x44kpreprocess > >> >> Cheers, >> >> - axel >> >> >> Axel Klenk >> Research Informatician >> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / >> Switzerland >> >> >> >> >> From: >> Alberto Goldoni <alberto.goldoni1975 at="" gmail.com=""> >> To: >> BioC <bioconductor at="" stat.math.ethz.ch=""> >> Date: >> 02.09.2010 15:38 >> Subject: >> [BioC] help with Agilent microarrays >> Sent by: >> bioconductor-bounces at stat.math.ethz.ch >> >> >> >> Hi to everybody, >> i'm analysing 2 color agilent microarrays (rgug4130a.db) and my >> targets.txt file is: >> >> "Name" "FileName" "Cy3" "Cy5" "GErep" >> "prova01" "p01.txt" "ref" "wt" 1 >> "prova02" "p02.txt" "ref" "wt" 1 >> "prova03" "p03.txt" "ref" "wt" 1 >> "prova04" "p04.txt" "ref" "ko" 2 >> "prova05" "p05.txt" "ref" "ko" 2 >> "prova06" "p06.txt" "ref" "ko" 2 >> >> now i have obtainet the data with "limma" and for the analysis i'm >> using "Agi4x44PreProcess" package. >> >> All works fine until the normalization: >> >> RG <- read.maimages(targets, source="agilent") >> >>> RG_NORM = BGandNorm(RG, BGmethod = "half", NORMmethod = "quantile", >> foreground = "MeanSignal", background = "BGMedianSignal", offset = 50, >> makePLOTpre = FALSE, makePLOTpost = FALSE) >> BACKGROUND CORRECTION AND NORMALIZATION >> >> foreground: MeanSignal >> background: BGMedianSignal >> >> BGmethod: half >> NORMmethod: quantile >> OUTPUT in log-2 scale >> >> ------------------------------------------------------ >> >> but when i'm tryng to do the filtering i obtain the follow error: >> >>> RGFILT = filter.probes(RG_NORM, control = TRUE, wellaboveBG = TRUE, >> isfound = TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE, > NonUnifOL >> = T, nas = TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limSAT = > 75, >> limPopnOL = 75, limNonUnifOL = 75, limNAS = 100, makePLOT = F, >> annotation.package = "rgug4130a.db", flag.counts = T, targets) >> FILTERING PROBES BY FLAGS >> >> >> FILTERING BY ControlType FLAG >> Error in data.frame(PROBE_ID, as.character(probe.chr), >> as.character(probe.seq), : >> arguments imply differing number of rows: 20500, 0 >> >> someone can help me??? >> >> best regards >> -- >> ----------------------------------------------------- >> Dr. Alberto Goldoni >> Parma, Italy >> >> _______________________________________________ >> 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 >> >> >> >> >> The information of this email and in any file transmitted with it is > strictly confidential and may be legally privileged. >> It is intended solely for the addressee. If you are not the intended > recipient, any copying, distribution or any other use of this email is > prohibited and may be unlawful. In such case, you should please notify the > sender immediately and destroy this email. >> The content of this email is not legally binding unless confirmed by > letter. >> Any views expressed in this message are those of the individual sender, > except where the message states otherwise and the sender is authorised to > state them to be the views of the sender's company. For further > information about Actelion please see our website at > http://www.actelion.com >> >> > > > > -- > ----------------------------------------------------- > Dr. Alberto Goldoni > Parma, Italy > ----------------------------------------------------- > > > > > The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. > It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. > The content of this email is not legally binding unless confirmed by letter. > Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com > > -- ----------------------------------------------------- Dr. Alberto Goldoni Parma, Italy ----------------------------------------------------- The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com