Entering edit mode
Vanessa Vermeirssen
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40
@vanessa-vermeirssen-2253
Last seen 10.2 years ago
Dear,
I have some questions about the marray Layout object. I try to upload
public microarray
data in R in order to create a microarray compendium.
I have used an SMD database file to create the targets, probes and
data
objects for marray.
The array has 21632 spots, however in the database file I only have
information for 21504 spots.
Moreover, some of the probes are not matchable to a gene and therefore
for those I would like to
neglect their expression values. I did this now by parsing the
database
file and setting the expression values
at NA for those "non-matchable" probes.
Hence I have 21504 probes, of which 801 are controls and 784 non-
matchable
(NAs in their expression values).
I tried to declare this with maSub that I use only part of the array
(21504 spots and not 21632).
My maControls only considers the 21504 spots.
I read in the whole thing and then look at the graphs created by one
color "image". There seems to be a lot
of white spots in my arrays and they are not consistent in the same
place on the array ( although all the NAs
refer to the same 784 probes in the 3 arrays, see code below).
I was wondering if this has something to do with this maSub... and
that
it put these NAs (21632-21504, only about 100 ones) randomly on the
array?
*How can I correctly read in my marrayLayout?*
I only want to use image to see if there is some spatial gradient in
my
arrays. If htere is, I need to use
background substraction, otherwise I won't.
This is the code I use...I am reading in 3 arrays of the format
Chalfie379.
In blue the output I get from R.
The pdf file with the M images can be found at
http://www.psb.ugent.be/~vamei/Docs/Chalfie379_image.pdf
library(limma)
library(marray)
library("Biobase")
Chalfie379targets=read.marrayInfo("file_A-SMDB-379", info.id=c(2,4,5),
labels=c(2))
summary(Chalfie379targets)
Object of class marrayInfo.
maLabels SMDfile green Cy3 CH1 red Cy5
CH2
1 new17040.xls new17040.xls wt sorted touch cell mutant sorted touch
cell
2 new17041.xls new17041.xls wt sorted touch cell mutant sorted touch
cell
3 new17042.xls new17042.xls wt sorted touch cell mutant sorted touch
cell
Number of labels: 3 Dimensions of maInfo matrix: 3 rows by 3
columns
Notes:
file_A-SMDB-379
file379 <- as.vector(Chalfie379targets at maInfo[,1])
Chalfie379.gnames <- read.marrayInfo(file379[1],info.id=c(1,2,3),
labels=2)
summary(Chalfie379.gnames)
Object of class marrayInfo.
maLabels Spot Name ID
1 AC3.5 1 AC3.5 AC3.5
2 AC3.8 2 AC3.8 AC3.8
3 AH6.6 3 AH6.6 AH6.6
4 B0001.3 4 B0001.3 B0001.3
5 B0024.1 5 B0024.1 B0024.1
6 B0024.4 6 B0024.4 B0024.4
7 C06H5.1 7 C06H5.1 C06H5.1
8 C07A9.5 8 C07A9.5 C07A9.5
9 C07G2.1 9 C07G2.1 C07G2.1
10 C08B6.4 10 C08B6.4 C08B6.4
...
Number of labels: 21504 Dimensions of maInfo matrix: 21504 rows by
3 columns
Notes:
new17040.xls
Chalfie379.L <- new("marrayLayout", maNgr=8, maNgc=4, maNsc=26,
maNsr=26)
maControls(Chalfie379.L) <- Chalfie379.gnames at maInfo[,3]
length(Chalfie379.L at maControls)
S <- c(1:maNspots(Chalfie379.L))
T <- Chalfie379.gnames at maInfo[,1]
Z <- S %in% T
maSub(Chalfie379.L) <- Z
ctl <- rep("control", length(T))
ctl[maControls(Chalfie379.L) != "control"] <- "probe"
maControls(Chalfie379.L) <- factor(ctl)
summary(Chalfie379.L)
Array layout: Object of class marrayLayout.
Total number of spots: 21632
Dimensions of grid matrix: 8 rows by 4 cols
Dimensions of spot matrices: 26 rows by 26 cols
Currently working with a subset of 21504spots.
Control spots:
There are 2 types of controls :
control probe
801 20703
Notes on layout:
Chalfie379.raw <- read.marrayRaw(file379,name.Gf="CH1_I",
name.Gb="CH1_B", name.Rf="CH2_I",
name.Rb="CH2_B", gnames=Chalfie379.gnames, layout=Chalfie379.L,
targets=Chalfie379targets, DEBUG=TRUE)
pdf("Chalfie379_image.pdf")
image(Chalfie379.raw, col=1, main="1")
image(Chalfie379.raw[,2], col=1, main="2")
image(Chalfie379.raw[,3], col=1, main="3")
dev.off()
myM <- Chalfie379.raw[,2]@maGf /Chalfie379.raw[,2]@maRf
sumis.na(myM))
[1] 784
> summary(whichis.na( Chalfie379.raw[,3]@maGf )))
Min. 1st Qu. Median Mean 3rd Qu. Max.
22 5564 10690 10770 15920 21450
> summary(whichis.na( Chalfie379.raw[,2]@maGf )))
Min. 1st Qu. Median Mean 3rd Qu. Max.
22 5564 10690 10770 15920 21450
> summary(whichis.na( Chalfie379.raw[,1]@maGf )))
Min. 1st Qu. Median Mean 3rd Qu. Max.
22 5564 10690 10770 15920 21450
Thank you so much for your help!
Best regards,
Vanessa Vermeirssen
--
--
==================================================================
Vanessa Vermeirssen, PhD
Tel:+32 (0)9 331 38 23 fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
vamei at psb.ugent.be http://www.psb.ugent.be
