Hi; Your diagnosis was correct! The first 114 files had accurate sizes while the rest of them had insufficient sizes. But I'm not so sure about disk space since, if this was the case, it is quite odd that the corrupted files had exactly the same size while not stopping in the middle of producing CEL files anyway. Right now, I'm in the middle of processing them and will update the result when done. This is just a reminder. Thanks,
TH 2010/5/11 Henrik Bengtsson <h...@stat.berkeley.edu> > On Tue, May 11, 2010 at 11:20 AM, Tae-Hoon Chung <hoontaech...@gmail.com> > wrote: > > Hi; > > > > This is what I got: > > > >> dataSet <- "HapMap500K,Sty"; > >> tags <- "ACC,-XY,BPN,-XY,RMA,A+B"; > >> chipType <- "Mapping250K_Sty"; > >> cdf <- AffymetrixCdfFile$byChipType(chipType); > >> cdfM <- getMonocellCdf(cdf); > >> ces <- CnChipEffectSet$byName(dataSet, tags=tags, cdf=cdfM, > >> mergeStrands=TRUE\ > > , combineAlleles=TRUE); > >> fileSizes <- sapply(ces, getFileSize); > >> print(getCdf(ces)); > > AffymetrixCdfFile: > > Path: annotationData/chipTypes/Mapping250K_Sty > > Filename: Mapping250K_Sty,monocell.CDF > > Filesize: 102.28MB > > Chip type: Mapping250K_Sty,monocell > > RAM: 0.00MB > > File format: v4 (binary; XDA) > > Dimension: 955x955 > > Number of cells: 912025 > > Number of units: 238378 > > Cells per unit: 3.83 > > Number of QC units: 6 > >> print(range(fileSizes)); > > [1] 686 9120944 > >> print(table(fileSizes)); > > fileSizes > > 686 9120944 > > 156 114 > > > > It seems like I got lots of corrupt files ... > > My guess is that the first 114 files are complete: > > print(table(fileSizes[1:114])); > > fileSizes > 9120944 > 114 > > and the last 156 files are incomplete: > > print(table(fileSizes[115:270])); > > fileSizes > 686 > 156 > > Is that the case? Did you by chance run out of disk space? That > would explain the result; there was enough to write the header of each > data file, but not the data section of each. I located this > possibility in the code and will add protection against it by first > generating a temporary file which is then renamed so that the creation > of the final file will become atomic and will not leave an incomplete > file behind. > > > > I think these had been generated before I updated aroma.affymetrix. > > I would generate them with updated library. > > Can I simply delete corresponding folders in probeData and plmData and > redo > > the whole procedure? > > Yes, that would solve it. It is enough to delete the plmData/ that > 'ces' refers to, i.e. getPath(ces). Keep the probeData/. > > Let us know how it goes. > > /Henrik > > > > > TH > > > > -- > > When reporting problems on aroma.affymetrix, make sure 1) to run the > latest > > version of the package, 2) to report the output of sessionInfo() and > > traceback(), and 3) to post a complete code example. > > > > > > You received this message because you are subscribed to the Google Groups > > "aroma.affymetrix" group with website http://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > -- Tae-Hoon Chung, PhD -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
