[BioC] Problem reading in files with marrayInput
James MacDonald
jmacdon at med.umich.edu
Tue Nov 4 15:17:14 MET 2003
I think your error is in the first line of your example. You are missing
a comma between info.id=1 and labels=1. Any time you see 'Error: syntax
error', you should look at the preceding line to see where the error
lies.
HTH,
Jim
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> Richard Friedman <friedman at cancercenter.columbia.edu> 11/03/03
05:21PM >>>
Fellow Expressionists,
I am attempting to duplicate the results of Dudoit,
Yang, and coworkers on the data of Callow as an exercise
for learning to use Spot with my own data. I have tried
a subset of six Spot Output files (3 WT, 3KO) as a proof
of concept. I am having difficulty reading in the files
correctly. I am running marrayInput downloaded on October 30,
2003, R1.8.0, and Windows XP. I would greatly appreciate it
if someone could tell me what I am doing incorrectly, suggest
something that I can do to debug the procedure, or be
willing to look at my input files to see if the problem lies
there. Here is a record of my session:
###########################################################
> array1.gnames <- read.marrayInfo(file.path(datadir, "array1.gdl"),
+ info.id =1 labels = 1, skip = 1)
Error: syntax error
> info.id =1, labels = 1, skip = 1)
Error: syntax error
> array1.gnames <- read.marrayInfo(file.path(datadir, "array1.gdl"),
+ info.id =1, labels = 1, skip = 1)
> array1.gnames
Object of class marrayInfo.
maLabels dat[, info.id]
1 2 2
2 3 3
3 4 4
4 5 5
5 6 6
6 7 7
7 8 8
8 9 9
9 10 10
10 11 11
...
Number of labels: 6383
Dimensions of maInfo matrix: 6383 rows by 1 columns
Notes:
C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.gdl
> help.start()
updating HTML package listing
updating HTML search index
If nothing happens, you should open `
C:\PROGRA~1\R\rw1080\doc\html\rwin.html ' yourself
> array1.gnames <- read.marrayInfo(file.path(datadir,
"array1.gdl"),info.id =6:8, labels = 6, skip = 1)
> array1.gnames
Object of class marrayInfo.
maLabels
1
Cy5RT
2
mSRB1
3
BLANK
4
BLANK
5
BLANK
6
7
5' similar to SW:BTF3_HUMAN P20290 TRANSCRIPTION FACTOR BTF3 ;.
gi|1287559|gb|W13502|W13502 [1287559]
8
5' similar to gb:J04794 ALCOHOL DEHYDROGENASE (HUMAN);.
gi|1287584|gb|W13547|W13547 [1287584]
9
5'. gi|1287586|gb|W13549|W13549 [1287586]
10 "5' similar to gb:X03747_cds1 SODIUM/POTASSIUM-TRANSPORTING ATPASE
BETA-1 (HUMAN); gb:X16646 Mouse mRNA for Na,K-ATPase beta subunit
(MOUSE);. gi|1315970|gb|W34060|W34060 [1315970]"
Cy3RT
1
Cy5RT
2
mSRB1
3
BLANK
4
BLANK
5
BLANK
6
7
5' similar to SW:BTF3_HUMAN P20290 TRANSCRIPTION FACTOR BTF3 ;.
gi|1287559|gb|W13502|W13502 [1287559]
8
5' similar to gb:J04794 ALCOHOL DEHYDROGENASE (HUMAN);.
gi|1287584|gb|W13547|W13547 [1287584]
9
5'. gi|1287586|gb|W13549|W13549 [1287586]
10 "5' similar to gb:X03747_cds1 SODIUM/POTASSIUM-TRANSPORTING ATPASE
BETA-1 (HUMAN); gb:X16646 Mouse mRNA for Na,K-ATPase beta subunit
(MOUSE);. gi|1315970|gb|W34060|W34060 [1315970]"
Control BLANK
1 Control BLANK
2 cDNA mSRB1
3 BLANK BLANK
4 BLANK BLANK
5 BLANK BLANK
6 cDNA 317448
7 cDNA 317452
8 cDNA 317456
9 cDNA 317460
10 cDNA 317464
...
Number of labels: 6383
Dimensions of maInfo matrix: 6383 rows by 3 columns
Notes:
C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.gdl
> array1.layout <- read.marrayLayout(fname = file.path(datadir,
+ "array1.gdl"), ngr =4, ngc = 4, nsr = 19, nsc =21, skip = 1,
+ ctrl.col =7, id.col = 6)
Error in scan(fname, quiet = TRUE, what = h, sep = sep, skip = skip +
:
unused argument(s) (ctrl.col ...)
> array1.layout <- read.marrayLayout(fname = file.path(datadir,
+ "array1.gdl"), ngr =4, ngc = 4, nsr = 19, nsc =21, skip = 1)
> array1.layout
Array layout: Object of class marrayLayout.
Total number of spots: 6384
Dimensions of grid matrix: 4 rows by 4 cols
Dimensions of spot matrices: 19 rows by 21 cols
Currently working with a subset of 6384 spots.
Control spots:
Notes on layout:
C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.gdl
> arrqy1.samples
Error: Object "arrqy1.samples" not found
> array1.samples
Object of class marrayInfo.
maLabels # of slide Names experiment Cy3 experiment Cy5
date comments
1 1 1 array1.1.spot wildtype ref
10/31/2003 NA
2 2 2 array1.2.spot wildtype ref
10/31/2003 NA
3 3 3 array1.3.spot wildtype ref
10/31/2003 NA
4 4 4 array1.4.spot ko ref
10/31/2003 NA
5 5 5 array1.5.spot ko ref
10/31/2003 NA
6 6 6 array1.6.spot ko ref
10/31/2003 NA
Number of labels: 6
Dimensions of maInfo matrix: 6 rows by 6 columns
Notes:
C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1Sample.txt
> fnames
[1] "array1.1.spot" "array1.2.spot" "array1.3.spot" "array1.4.spot"
"array1.5.spot" "array1.6.spot"
> array1.raw <- read.marrayRaw(fnames, path = datadir, name.Gf =
"Gmean",
+ name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR",
+ layout = array1.layout, gnames = array1.gnames, targets =
array1.samples)
[1] "Reading
C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot"
[1] "Reading
C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot"
[1] "Reading
C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot"
[1] "Reading
C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot"
[1] "Reading
C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot"
[1] "Reading
C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot"
Warning messages:
1: number of items read is not a multiple of the number of columns
2: number of rows of result
is not a multiple of vector length (arg 2) in: cbind(Gf,
as.numeric(dat[[name.Gf]]))
3: number of rows of result
is not a multiple of vector length (arg 2) in: cbind(Gb,
as.numeric(dat[[name.Gb]]))
4: number of rows of result
is not a multiple of vector length (arg 2) in: cbind(Rf,
as.numeric(dat[[name.Rf]]))
5: number of rows of result
is not a multiple of vector length (arg 2) in: cbind(Rb,
as.numeric(dat[[name.Rb]]))
>
##############################################################
Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/
"Everybody is going to do their book reports on Harry Potter.
I'm going to do mine on 'Red Planet'." -Isaac Friedman, age 13
(I know I said "no more Isaac quotes", but I couldn't resist that
one).
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