[BioC] cellHTS readPlateList funciton cannot find files

Ian Sudbery ims at sanger.ac.uk
Wed Jun 24 23:37:35 CEST 2009


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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