[BioC] cellHTS readPlateList funciton cannot find files
Ian Sudbery
ims at sanger.ac.uk
Thu Jun 25 01:32:32 CEST 2009
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
>
>
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