Question: arrayQualityMetrics error with one color array and log transform
1
gravatar for daugherty_a
4.8 years ago by
United States
daugherty_a0 wrote:

Hi all,

   I'm a new to arrayQualityMetrics, so hopefully this isn't an obvious question, but I've been getting the error below when I attempt to run arrayQualityMetrics on several GEO files, including: GDS961 and GDS4012.

The error I've received is:

Error in x[pos] = log2(x[pos]) : 
  NAs are not allowed in subscripted assignments
Calls: runArrayQC ... platformspecific -> platformspecific -> oneColor -> logtransform

 

And my session info:

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] org.Hs.eg.db_3.0.0         RSQLite_0.11.4
 [3] AnnotationDbi_1.28.0       GenomeInfoDb_1.2.0
 [5] IRanges_2.0.0              S4Vectors_0.4.0
 [7] samr_2.0                   matrixStats_0.10.3
 [9] impute_1.40.0              GEOquery_2.32.0
[11] Biobase_2.26.0             BiocGenerics_0.12.0
[13] RMySQL_0.9-3               DBI_0.3.1
[15] arrayQualityMetrics_3.22.0

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3       affy_1.44.0           affyio_1.34.0
 [4] affyPLM_1.42.0        annotate_1.44.0       base64_1.1
 [7] beadarray_2.16.0      BeadDataPackR_1.18.0  BiocInstaller_1.16.0
[10] Biostrings_2.34.0     Cairo_1.5-6           cluster_1.15.3
[13] colorspace_1.2-4      foreign_0.8-61        Formula_1.1-2
[16] gcrma_2.38.0          genefilter_1.48.1     GenomicRanges_1.18.1
[19] grid_3.1.1            gridSVG_1.4-0         Hmisc_3.14-5
[22] hwriter_1.3.2         illuminaio_0.8.0      lattice_0.20-29
[25] latticeExtra_0.6-26   limma_3.22.1          nnet_7.3-8
[28] plyr_1.8.1            preprocessCore_1.28.0 RColorBrewer_1.0-5
[31] Rcpp_0.11.3           RCurl_1.95-4.3        reshape2_1.4
[34] RJSONIO_1.3-0         R.methodsS3_1.6.1     rpart_4.1-8
[37] setRNG_2011.11-2      splines_3.1.1         stringr_0.6.2
[40] survival_2.37-7       SVGAnnotation_0.93-1  vsn_3.34.0
[43] XML_3.98-1.1          xtable_1.7-4          XVector_0.6.0
[46] zlibbioc_1.12.0

 

 

Thanks for any and all help or tips!

 

 

ADD COMMENTlink modified 4.8 years ago by James W. MacDonald50k • written 4.8 years ago by daugherty_a0

Please post the code that leads up to the error, not just the error. Thanks!

ADD REPLYlink written 4.8 years ago by Dan Tenenbaum8.2k
Answer: arrayQualityMetrics error with one color array and log transform
3
gravatar for James W. MacDonald
4.8 years ago by
United States
James W. MacDonald50k wrote:

There are NA values in the data you have downloaded:

> z <- getGEO("GSE1009")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1009/matrix/
Found 1 file(s)
GSE1009_series_matrix.txt.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  225k  100  225k    0     0   127k      0  0:00:01  0:00:01 --:--:--  127k
File stored at:
/data3/tmp/RtmptO3qLR/GPL8300.soft

> naind <- apply(exprs(z[[1]]), 1, function(x) any(is.na(x))) 
> exprs(z[[1]])[naind,] 
GSM15965 GSM15966 GSM15967 GSM15968 GSM15969 GSM15970 
NA 10085.0 8665.6 378.1 707.3 758.1 
> arrayQualityMetrics(z[[1]][!naind,], do.logtransform=TRUE)
The directory 'arrayQualityMetrics report for z[[1]][!naind, ]' has been created.

I wouldn't, in general, rely upon some MAS5.0 data from 2004. Instead, you can get the raw data and use something more modern like RMA:

> zz <- getGEOSuppFiles("GSE1009")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1009/suppl/
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 17.6M  100 17.6M    0     0  5708k      0  0:00:03  0:00:03 --:--:-- 5709k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   409  100   409    0     0    373      0  0:00:01  0:00:01 --:--:--   373

> setwd("GSE1009/")
> untar("GSE1009_RAW.tar")
> library(affy)
> dat <- ReadAffy()
> eset <- rma(dat)
Background correcting
Normalizing
Calculating Expression
> arrayQualityMetrics(eset)
The directory 'arrayQualityMetrics report for eset' has been created.

 

ADD COMMENTlink written 4.8 years ago by James W. MacDonald50k

Thanks for the help.  We seem to keep running into issues with older data giving us issues, so you're suggestion of switching over to RMA is much appreciated!

ADD REPLYlink written 4.8 years ago by daugherty_a0
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