Hi, I'm trying to us cellHTS2 to analysis screening data. I have a plate list file (called final_platelist) with 72 files in it, the first few rows of which look like: Filename Plate Replicate Channel Batch 1a1.before 1 1 1 1 1a1.after 1 1 2 1 1a2.before 1 2 1 1 1a2.after 1 2 2 1 1b1.before 2 1 1 1 1b1.after 2 1 2 1 1b2.before 2 2 1 1 1b2.after 2 2 2 1 2a1.before 3 1 1 1 2a1.after 3 1 2 1 2a2.before 3 2 1 1 when I try to read the plate list file with either x<- readPlateList("final_platelist", name = "Screen") or dataPath = "D:/analysis" x<- readPlateList("final_platelist", name = "Screen", path = dataPath) I get screen: found data in 8 x 12 (96 well) format. Reading 1: 1a1.before Reading 2: 1a1.after Reading 3: 1a2.before Reading 4: 1a2.after Reading 5: 1b1.before Reading 6: 1b1.after Reading 7: 1b2.before Reading 8: 1b2.after Reading 9: 2a1.before Reading 10: 2a1.after Reading 11: 2a2.before Reading 12: 2a2.after Reading 13: 2b1.before Reading 14: 2b2.before Reading 15: 2b2.4.after Reading 16: 2b2.1.after Reading 17: 3a1.before Reading 18: 3a2.before Reading 19: 3a2.2.after Reading 20: 3a2.4after Reading 21: 3b1.before Reading 22: 3b2.before Reading 23: 3b2.3.after Reading 24: 3b2.6.after Reading 25: 3.1.before Reading 26: 3.1.after Reading 27: 3.2.before Reading 28: 3.2.after Reading 29: 3.3.before Reading 30: 3.3.after Reading 31: 3.4.before Reading 32: 3.4.after Reading 33: 3.5.before Reading 34: 3.5.after Reading 35: 3.6.before Reading 36: 3.6.after Reading 37: 5b1.before Reading 38: 5b1.after Reading 39: 5b2.before Reading 40: 5b2.after Reading 41: 6a1.before Reading 42: 6a1.after Reading 43: 6a2.before Reading 44: 6a2.after Reading 45: 6b1.before Reading 46: 6b1.after Reading 47: 6b2.before Reading 48: 6b2.after Reading 49: 7a1.before Reading 50: 7a1.after Reading 51: 7a2.before Reading 52: 7a2.after Reading 53: 7b1.before Reading 54: 7b1.after Reading 55: 7b2.before Reading 56: 7b2.after Reading 57: 8a1.before Reading 58: 8a1.after Reading 59: 8a2.before Reading 60: 8a2.after Reading 61: 8b1.before Reading 62: 8b1.after Reading 63: 8b2.before Reading 64: 8b2.after Reading 65: 9a1.before Reading 66: 9a1.after Reading 67: 9a2.before Reading 68: 9a2.after Reading 69: 9b1.before Reading 70: 9b1.after Reading 71: 9b2.before Reading 72: 9b2.after Read 72 plates. Warning message: Please check the following problems encountered while reading the data: Filename Error 1a1.before File not found: D:/analysis/1a1.before 1a1.after File not found: D:/analysis/1a1.after 1a2.before File not found: D:/analysis/1a2.before 1a2.after File not found: D:/analysis/1a2.after 1b1.before File not found: D:/analysis/1b1.before ...and 66 more. which is all the files. Looking at the code for readPlateList, it looks like it should return "None of the files were found in the given 'path': %s" if I can't find any of the files. If I try: read.table("D:/analysis/1a1.before") or read.table("1a1.before") I get: V1 V2 V3 1 1a1.before.txt A01 13407.0465 2 1a1.before.txt A02 14731.2945 3 1a1.before.txt A03 13690.2735 4 1a1.before.txt A04 13900.3165 5 1a1.before.txt A05 14780.1435 6 1a1.before.txt A06 13716.4025 7 1a1.before.txt A07 13642.0305 8 1a1.before.txt A08 14574.3585 9 1a1.before.txt A09 14529.6605 10 1a1.before.txt A10 15081.6405 11 1a1.before.txt A11 14907.5285 12 1a1.before.txt A12 43.3555 13 1a1.before.txt B01 14503.9395 14 1a1.before.txt B02 15486.6975 and the rest of the plate. Does anyone have any idea what is happening? Ian Sudbery ------------- Wellcome Trust Sanger Institute > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] cellHTS2_2.8.1 hwriter_1.1 vsn_3.12.0 splots_1.10.0 [5] genefilter_1.24.2 Biobase_2.4.1 RColorBrewer_1.0-2 loaded via a namespace (and not attached): [1] affy_1.22.0 affyio_1.12.0 annotate_1.22.0 [4] AnnotationDbi_1.6.1 DBI_0.2-4 lattice_0.17-22 [7] limma_2.18.2 MASS_7.2-46 prada_1.20.0 [10] preprocessCore_1.6.0 rrcov_0.5-01 RSQLite_0.7-1 [13] splines_2.9.0 stats4_2.9.0 survival_2.35-4 [16] xtable_1.5-5 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

After Studying the code of readPlateList some more, I tracked the error down. The function locates the filename within the directory by greping the filename against the directory. If it doesn't find exactly one match then it returns "File not found". However, this directory contains longer filenames that contain the shorter filenames which represent the files being read in. e.g. I'm trying to read in 1a1.before. But the directory also contains 1a1.before.txt. greping the directory with 1a1.before returns both files and so breaks the function. This must be a bug right? Ian Sudbery ------------ Ian Sudbery wrote: > Hi, > > I'm trying to us cellHTS2 to analysis screening data. > > I have a plate list file (called final_platelist) with 72 files in it, > the first few rows of which look like: > > Filename Plate Replicate Channel Batch > 1a1.before 1 1 1 1 > 1a1.after 1 1 2 1 > 1a2.before 1 2 1 1 > 1a2.after 1 2 2 1 > 1b1.before 2 1 1 1 > 1b1.after 2 1 2 1 > 1b2.before 2 2 1 1 > 1b2.after 2 2 2 1 > 2a1.before 3 1 1 1 > 2a1.after 3 1 2 1 > 2a2.before 3 2 1 1 > > when I try to read the plate list file with either > > x<- readPlateList("final_platelist", name = "Screen") > > or > > dataPath = "D:/analysis" > > x<- readPlateList("final_platelist", name = "Screen", path = dataPath) > > I get > screen: found data in 8 x 12 (96 well) format. > > Reading 1: 1a1.before > Reading 2: 1a1.after > Reading 3: 1a2.before > Reading 4: 1a2.after > Reading 5: 1b1.before > Reading 6: 1b1.after > Reading 7: 1b2.before > Reading 8: 1b2.after > Reading 9: 2a1.before > Reading 10: 2a1.after > Reading 11: 2a2.before > Reading 12: 2a2.after > Reading 13: 2b1.before > Reading 14: 2b2.before > Reading 15: 2b2.4.after > Reading 16: 2b2.1.after > Reading 17: 3a1.before > Reading 18: 3a2.before > Reading 19: 3a2.2.after > Reading 20: 3a2.4after > Reading 21: 3b1.before > Reading 22: 3b2.before > Reading 23: 3b2.3.after > Reading 24: 3b2.6.after > Reading 25: 3.1.before > Reading 26: 3.1.after > Reading 27: 3.2.before > Reading 28: 3.2.after > Reading 29: 3.3.before > Reading 30: 3.3.after > Reading 31: 3.4.before > Reading 32: 3.4.after > Reading 33: 3.5.before > Reading 34: 3.5.after > Reading 35: 3.6.before > Reading 36: 3.6.after > Reading 37: 5b1.before > Reading 38: 5b1.after > Reading 39: 5b2.before > Reading 40: 5b2.after > Reading 41: 6a1.before > Reading 42: 6a1.after > Reading 43: 6a2.before > Reading 44: 6a2.after > Reading 45: 6b1.before > Reading 46: 6b1.after > Reading 47: 6b2.before > Reading 48: 6b2.after > Reading 49: 7a1.before > Reading 50: 7a1.after > Reading 51: 7a2.before > Reading 52: 7a2.after > Reading 53: 7b1.before > Reading 54: 7b1.after > Reading 55: 7b2.before > Reading 56: 7b2.after > Reading 57: 8a1.before > Reading 58: 8a1.after > Reading 59: 8a2.before > Reading 60: 8a2.after > Reading 61: 8b1.before > Reading 62: 8b1.after > Reading 63: 8b2.before > Reading 64: 8b2.after > Reading 65: 9a1.before > Reading 66: 9a1.after > Reading 67: 9a2.before > Reading 68: 9a2.after > Reading 69: 9b1.before > Reading 70: 9b1.after > Reading 71: 9b2.before > Reading 72: 9b2.after > Read 72 plates. > Warning message: > Please check the following problems encountered while reading the data: > Filename Error > 1a1.before File not found: D:/analysis/1a1.before > 1a1.after File not found: D:/analysis/1a1.after > 1a2.before File not found: D:/analysis/1a2.before > 1a2.after File not found: D:/analysis/1a2.after > 1b1.before File not found: D:/analysis/1b1.before > ...and 66 more. > > > which is all the files. Looking at the code for readPlateList, it > looks like it should return "None of the files were found in the given > 'path': %s" if I can't find any of the files. > > If I try: > > read.table("D:/analysis/1a1.before") > > or > > read.table("1a1.before") > > I get: > > V1 V2 V3 > 1 1a1.before.txt A01 13407.0465 > 2 1a1.before.txt A02 14731.2945 > 3 1a1.before.txt A03 13690.2735 > 4 1a1.before.txt A04 13900.3165 > 5 1a1.before.txt A05 14780.1435 > 6 1a1.before.txt A06 13716.4025 > 7 1a1.before.txt A07 13642.0305 > 8 1a1.before.txt A08 14574.3585 > 9 1a1.before.txt A09 14529.6605 > 10 1a1.before.txt A10 15081.6405 > 11 1a1.before.txt A11 14907.5285 > 12 1a1.before.txt A12 43.3555 > 13 1a1.before.txt B01 14503.9395 > 14 1a1.before.txt B02 15486.6975 > > > and the rest of the plate. > > Does anyone have any idea what is happening? > > Ian Sudbery > ------------- > > Wellcome Trust Sanger Institute > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods [8] base > other attached packages: > [1] cellHTS2_2.8.1 hwriter_1.1 vsn_3.12.0 > splots_1.10.0 [5] genefilter_1.24.2 Biobase_2.4.1 > RColorBrewer_1.0-2 > > loaded via a namespace (and not attached): > [1] affy_1.22.0 affyio_1.12.0 annotate_1.22.0 [4] > AnnotationDbi_1.6.1 DBI_0.2-4 lattice_0.17-22 [7] > limma_2.18.2 MASS_7.2-46 prada_1.20.0 [10] > preprocessCore_1.6.0 rrcov_0.5-01 RSQLite_0.7-1 [13] > splines_2.9.0 stats4_2.9.0 survival_2.35-4 [16] > xtable_1.5-5 > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.