[BioC] Problem reading in files with marrayInput
Richard Friedman
friedman at cancercenter.columbia.edu
Mon Nov 3 23:21:30 MET 2003
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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