filtered CDF file results in errors
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@sebastien-gerega-2229
Last seen 8.1 years ago
Hi, I am working on the yeast2 affymetrix chip and am trying to filter out all the s_pombe probes with the following code: library(altcdfenvs) bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf") pp = read.table("s_pombe.msk", sep="\t", skip=2) ids = as.character(pp[,1]) saccdf = bothcdf[ids] print(bothcdf) print(saccdf) saccdf at envName = "Sac ids only" envsaccdf = as(saccdf, "environment") data = ReadAffy(filenames=filenames) data at cdfName <- "envsaccdf" "s_pombe.msk" was downloaded from the Affymetrix website and contains a list of all the s_cerevisiae probes (those I want to use). This code runs without problems but once I get to QC I get the following error: hist(data, main="Log2(Intensity)", col=targetCol) Error in density.default(newX[, i], ...) : 'x' contains missing values I have tried running the reverse analysis, that is filtering out the s_cerevisiae probes instead of the s_pombe ones and I no longer get the error. What could be going wrong? Can anyone give me some tips to troubleshoot the problem? thanks in advance, Seb
yeast2 cdf yeast2 cdf • 766 views
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@sebastien-gerega-2229
Last seen 8.1 years ago
Hi, I am working on the yeast2 affymetrix chip and am trying to filter out all the s_pombe probes with the following code: library(altcdfenvs) bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf") pp = read.table("s_pombe.msk", sep="\t", skip=2) ids = as.character(pp[,1]) saccdf = bothcdf[ids] print(bothcdf) print(saccdf) saccdf <at> envName = "Sac ids only" envsaccdf = as(saccdf, "environment") data = ReadAffy(filenames=filenames) data <at> cdfName <- "envsaccdf" "s_pombe.msk" was downloaded from the Affymetrix website and contains a list of all the s_cerevisiae probes (those I want to use). This code runs without problems but once I get to QC I get the following error: hist(data, main="Log2(Intensity)", col=targetCol) Error in density.default(newX[, i], ...) : 'x' contains missing values I have tried running the reverse analysis, that is filtering out the s_cerevisiae probes instead of the s_pombe ones and I no longer get the error. What could be going wrong? Can anyone give me some tips to troubleshoot the problem? thanks in advance, Seb I have tried again using the new BioC release and no longer get an error when creating the histogram. However, now when I run fitPLM on the AffyBatch object R completely crashes. If I run fitPLM on the AffyBatch without having changed the CDF environment I get no problems. Does anyone have any ideas what might be causing this? or how I could deal with the problem? thanks, Seb
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Sebastien Gerega wrote: > Hi, > I am working on the yeast2 affymetrix chip and am trying to filter out > all the s_pombe probes with the following code: > > library(altcdfenvs) > bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf") > pp = read.table("s_pombe.msk", sep="\t", skip=2) > ids = as.character(pp[,1]) > saccdf = bothcdf[ids] > print(bothcdf) > print(saccdf) > saccdf <at> envName = "Sac ids only" > envsaccdf = as(saccdf, "environment") > data = ReadAffy(filenames=filenames) > data at cdfName <- "envsaccdf" > > "s_pombe.msk" was downloaded from the Affymetrix website and contains > a list of all the s_cerevisiae probes (those I want to use). > > This code runs without problems but once I get to QC I get the > following error: > hist(data, main="Log2(Intensity)", col=targetCol) > Error in density.default(newX[, i], ...) : 'x' contains missing values > > I have tried running the reverse analysis, that is filtering out the > s_cerevisiae probes instead of the s_pombe ones and I no longer get > the error. > What could be going wrong? Can anyone give me some tips to > troubleshoot the problem? > thanks in advance, > Seb > > > I have tried again using the new BioC release and no longer get an > error when creating the histogram. > However, now when I run fitPLM on the AffyBatch object R completely > crashes. If I run fitPLM on the AffyBatch without having changed the > CDF environment I get no problems. > Does anyone have any ideas what might be causing this? or how I could > deal with the problem? > thanks, > Seb > > I seem to have resolved this problem by removing the probes listed in "s_cerevisiae.msk" rather than using those listed in "s_pombe.msk" with the following code: bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf") pp = read.table("s_cerevisiae.msk", sep="\t", skip=2) ids = geneNames(bothcdf)[which(geneNames(bothcdf) %in% pp[,1] == FALSE)] saccdf = bothcdf[ids] print(bothcdf) print(saccdf) saccdf at envName = "Sac ids only" envsaccdf = as(saccdf, "environment") However, I am still curious what was causing the problem....
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> Sebastien Gerega wrote: >> Hi, >> I am working on the yeast2 affymetrix chip and am trying to filter out >> all the s_pombe probes with the following code: >> >> library(altcdfenvs) >> bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf") >> pp = read.table("s_pombe.msk", sep="\t", skip=2) >> ids = as.character(pp[,1]) >> saccdf = bothcdf[ids] >> print(bothcdf) >> print(saccdf) >> saccdf <at> envName = "Sac ids only" >> envsaccdf = as(saccdf, "environment") >> data = ReadAffy(filenames=filenames) >> data at cdfName <- "envsaccdf" >> >> "s_pombe.msk" was downloaded from the Affymetrix website and contains >> a list of all the s_cerevisiae probes (those I want to use). >> >> This code runs without problems but once I get to QC I get the >> following error: >> hist(data, main="Log2(Intensity)", col=targetCol) >> Error in density.default(newX[, i], ...) : 'x' contains missing values >> >> I have tried running the reverse analysis, that is filtering out the >> s_cerevisiae probes instead of the s_pombe ones and I no longer get >> the error. >> What could be going wrong? Can anyone give me some tips to >> troubleshoot the problem? >> thanks in advance, >> Seb >> >> >> I have tried again using the new BioC release and no longer get an >> error when creating the histogram. >> However, now when I run fitPLM on the AffyBatch object R completely >> crashes. If I run fitPLM on the AffyBatch without having changed the >> CDF environment I get no problems. >> Does anyone have any ideas what might be causing this? or how I could >> deal with the problem? >> thanks, >> Seb >> >> > I seem to have resolved this problem by removing the probes listed in > "s_cerevisiae.msk" rather than using those listed in "s_pombe.msk" with > the following code: > > bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf") > pp = read.table("s_cerevisiae.msk", sep="\t", skip=2) > ids = geneNames(bothcdf)[which(geneNames(bothcdf) %in% pp[,1] == FALSE)] > saccdf = bothcdf[ids] > print(bothcdf) > print(saccdf) > saccdf at envName = "Sac ids only" > envsaccdf = as(saccdf, "environment") > > However, I am still curious what was causing the problem.... > Could you make available the files needed to reproduce the problem ? (we can sort the details of data transfer off-list). Thanks, L.
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