Entering edit mode
Asta Laiho
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70
@asta-laiho-2025
Last seen 10.2 years ago
I am using beadarray to read in raw data from two Illumina mouse 6
bead chips.
I am trying to read in 4 arrays (two arrays per sample) per chip.
However, there
is a problem I didn't manage to solve when I try to combine the data
sets from two
different chips.
Combining the different data sets works if I don't give anything for
the 'arrayNames'
parameter in readIllumina() but then all the files in the directory
are read.
This small data set is only for testing and in the future I would like
to combine many
chips into one object, not necessarily including every sample on each
array.
Thanks in advance,
Asta
Below is the code and session information.
---
library(beadarray)
data <- readIllumina(path="1735640017",
textType=".txt",
arrayNames=c("1735640017_A_1", "1735640017_A_2",
"1735640017_D_1", "1735640017_D_2")
)
Found 4 arrays
Reading pixels of 1735640017/1735640017_A_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640017/1735640017_A_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640017/1735640017_D_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640017/1735640017_D_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
data <- createBeadSummaryData(data, imagesPerArray = 2)
exprs(data)[1:10,]
1735640017_A_1 1735640017_D_1
10243 148.28308 157.3592
10280 96.39223 108.3309
10575 132.72321 136.9459
20048 106.45987 125.9253
20296 12385.10467 11879.6216
20343 470.61351 293.3878
20373 114.44354 133.7846
20431 25695.85350 30478.6505
50008 607.38792 631.1659
50014 86.33236 89.1350
data2 <- readIllumina(path="1735640018",
textType=".txt",
arrayNames=c("1735640018_A_1", "1735640018_A_2",
"1735640018_D_1", "1735640018_D_2")
)
Found 4 arrays
arrayNames(dataReading pixels of 1735640018/1735640018_A_1_Grn.tif
2)
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640018/1735640018_A_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640018/1735640018_D_1_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
Reading pixels of 1735640018/1735640018_D_2_Grn.tif
Calculating background
Sharpening Image
Calculating foregound
Background correcting: method = subtract
data2 <- createBeadSummaryData(data2, imagesPerArray = 2)
exprs(data2)[1:10,]
1735640018_A_1 1735640018_D_1
10243 147.6654 153.04544
10280 113.3786 101.17059
10575 130.5891 123.23560
20048 113.0089 114.82174
20296 12992.2415 9307.39043
20343 336.2219 415.96840
20373 110.7654 115.41545
20431 27717.1189 16975.48752
50008 550.6863 542.58111
50014 92.1901 80.69506
combinedData <- combine(data, data2)
Error in combine(pDataX, pDataY) : data.frames contain conflicting
data:
non-conforming colname(s): arrayName
#---------------------------------------------------------------------
------
> sessionInfo()
R version 2.5.0 (2007-04-23)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
.UTF-8;
LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L
C_NAME=C;
LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI
ON=C
attached base packages:
[1] "tools" "stats" "graphics" "grDevices" "utils"
"datasets"
[7] "methods" "base"
other attached packages:
beadarray affy affyio geneplotter lattice
annotate
"1.5.14" "1.14.0" "1.4.0" "1.14.0" "0.15-4"
"1.14.1"
Biobase limma
"1.14.0" "2.10.0"