Imputation problem in aCGH
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Entering edit mode
Benjamin Otto ▴ 830
@benjamin-otto-1519
Last seen 7.1 years ago
Dear bioconductors, Trying to impute some log2 ratios with the lowess imputation I get the following error message, which I can't correlate with my data provided: # Processing chromosome 2 # Error in approx(lowess(kbl[ind], vecl[ind], f = smooth), xout = kbl[-ind]) : # need at least two non-NA values to interpolate Now here are two sets of data. The first results in the error message the second one runs perfectly. Set #1 (the failing one): > mx.ratios X1874 X2130 AL137761 -0.104402 -0.231907 BC040221 0.520388 0.204723 NM_015677 NA 0.038293 M83653 0.133378 NA BC033490 0.227578 -0.092427 > mx.info Clone Chrom kb AL137761 AL137761 2 29114 BC040221 BC040221 2 184720 NM_015677 NM_015677 2 219977 M83653 M83653 2 267639 BC033490 BC033490 2 270090 Set #2 (the working one): > my.ratios X1874 X2130 NM_015677 NA 0.038293 M83653 0.133378 NA BC033490 0.227578 -0.092427 AK091892 -0.177032 -0.078277 AW451118 -0.092482 0.019423 > my.info Clone Chrom kb NM_015677 NM_015677 2 219977 M83653 M83653 2 267639 BC033490 BC033490 2 270090 AK091892 AK091892 2 293681 AW451118 AW451118 2 482546 The commands used are: > mx <- create.aCGH(mx.ratios,mx.info) > impute.lowess(mx) Processing chromosome 2 Error in approx(lowess(kbl[ind], vecl[ind], f = smooth), xout = kbl[-ind]) : need at least two non-NA values to interpolate SESSIONINFO: ============ R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "tools" "splines" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: aCGH sma multtest Biobase survival cluster hgu133plus2 "1.10.0" "0.5.15" "1.14.0" "1.14.0" "2.31" "1.11.5" "1.16.0" Has anyone an idea what the cause of the error is and why I don't get it in the second set? I don't see any significant difference... Best regards, Benjamin Otto ====================================== Benjamin Otto University Hospital Hamburg-Eppendorf Institute For Clinical Chemistry Martinistr. 52 D-20246 Hamburg Tel.: +49 40 42803 1908 Fax.: +49 40 42803 4971 ====================================== -- Pflichtangaben gem?? Gesetz ?ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universit?tsklinikum Hamburg-Eppendorf K?rperschaft des ?ffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. J?rg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus
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Entering edit mode
Benjamin Otto ▴ 830
@benjamin-otto-1519
Last seen 7.1 years ago
Hi, I just found out what the problem is, however a new question arises here. My chromosomal location provided was in bp not kb. During the imputation the impute.lowess function segments each chromosome into the two arms using a included list of centomere locations. At the moment I provide a chromosome which has only one resident on one of the arms the function moans because it needs at least two non NA-Values. Right so this is the old problem. When I had a look at the centromere locations I found the locations diverging from the positions given by ensemble. Now how does the function discriminate between the organisms? It seems that it doesn't and if that is so, then isn't the the separation into the two arms more a downside than an advantage? Cheers, Benjamin -----Urspr?ngliche Nachricht----- Von: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Benjamin Otto Gesendet: Tuesday, July 17, 2007 11:24 AM An: bioconductor at stat.math.ethz.ch Betreff: [BioC] Imputation problem in aCGH Dear bioconductors, Trying to impute some log2 ratios with the lowess imputation I get the following error message, which I can't correlate with my data provided: # Processing chromosome 2 # Error in approx(lowess(kbl[ind], vecl[ind], f = smooth), xout = kbl[-ind]) : # need at least two non-NA values to interpolate Now here are two sets of data. The first results in the error message the second one runs perfectly. Set #1 (the failing one): > mx.ratios X1874 X2130 AL137761 -0.104402 -0.231907 BC040221 0.520388 0.204723 NM_015677 NA 0.038293 M83653 0.133378 NA BC033490 0.227578 -0.092427 > mx.info Clone Chrom kb AL137761 AL137761 2 29114 BC040221 BC040221 2 184720 NM_015677 NM_015677 2 219977 M83653 M83653 2 267639 BC033490 BC033490 2 270090 Set #2 (the working one): > my.ratios X1874 X2130 NM_015677 NA 0.038293 M83653 0.133378 NA BC033490 0.227578 -0.092427 AK091892 -0.177032 -0.078277 AW451118 -0.092482 0.019423 > my.info Clone Chrom kb NM_015677 NM_015677 2 219977 M83653 M83653 2 267639 BC033490 BC033490 2 270090 AK091892 AK091892 2 293681 AW451118 AW451118 2 482546 The commands used are: > mx <- create.aCGH(mx.ratios,mx.info) > impute.lowess(mx) Processing chromosome 2 Error in approx(lowess(kbl[ind], vecl[ind], f = smooth), xout = kbl[-ind]) : need at least two non-NA values to interpolate SESSIONINFO: ============ R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "tools" "splines" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: aCGH sma multtest Biobase survival cluster hgu133plus2 "1.10.0" "0.5.15" "1.14.0" "1.14.0" "2.31" "1.11.5" "1.16.0" Has anyone an idea what the cause of the error is and why I don't get it in the second set? I don't see any significant difference... Best regards, Benjamin Otto ====================================== Benjamin Otto University Hospital Hamburg-Eppendorf Institute For Clinical Chemistry Martinistr. 52 D-20246 Hamburg Tel.: +49 40 42803 1908 Fax.: +49 40 42803 4971 ====================================== -- Pflichtangaben gemd_ Gesetz |ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitdtsklinikum Hamburg-Eppendorf Kvrperschaft des vffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Jvrg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus -- Pflichtangaben gem?? Gesetz ?ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universit?tsklinikum Hamburg-Eppendorf K?rperschaft des ?ffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. J?rg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus