[BioC] remove duplicated rows generated by read.ilmn()

[Rao,Xiayu]

Hello,

Sorry for my last email. The extra rows are pointing to the control probes, which will be gone after background correction and normalization by neqc().

Thanks,
Xiayu  

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Rao,Xiayu
Sent: Tuesday, July 29, 2014 12:59 PM
To: 'bioconductor at r-project.org'
Subject: [BioC] remove duplicated rows generated by read.ilmn()

Hello,

It is interesting to see that read.ilmn() generates some extra rows. It turns out that the extra rows are duplicates, possibly due to the different decimal points from different data sets when I combined the data from different chips together. How do I remove the duplicates (keep only the first row) for the ElistRaw class, x ??

I simply merged different data sets to keep only shared probeIDs and SYMBOLs, and I removed the rows with blank values for the SYMBOL column.

library(limma)
x <- read.ilmn(files="all_samples.txt",ctrlfiles="all_samples_cont.txt",other.columns="Detection")
x

> x$E[rownames(x$E)=="1430239",]
        X8508853077_D X8508853077_G X8909358290_B X8909358290_C X8909358290_E X8909358290_F X8909358290_G X8909358290_H X8909358290_I
1430239      9375.439      6950.326      2623.736      2923.202      13051.55      9663.131      9752.901      6377.608      7601.526
1430239      9375.400      6950.300      2623.700      2923.200      13051.60      9663.100      9752.900      6377.600      7601.500
        X167.H1 X403.H1 X495.E6 X527.E5 X544.B8 X619.C7 X625.D3 X340.H1 X648.B4
1430239 11586.2 12608.4 13100.6 10750.6 13198.5 12399.2 17938.1 14340.3   17329
1430239 11586.2 12608.4 13100.6 10750.6 13198.5 12399.2 17938.1 14340.3   17329

NOTE: R and limma are in the latest version.
Thank you very much!

Thanks,
Xiayu

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