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!

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.