Question

Affymetrix ReadAffy() can't read my CEL file

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Entering edit mode

kanacska ▴ 10

@kanacska-7375

Last seen 8.6 years ago

Hungary

Hi!

I'm using R-3.1.2 in R studio.

I wan't to use ReadAffy() , but it doesn't work

> # Read in the CEL files in the directory
> raw <- ReadAffy(compress=gzipped, sampleNames = sNames)
Error in value[[3L]](cond) : row names contain missing values
AnnotatedDataFrame 'initialize' could not update varMetadata:
perhaps pData and varMetadata are inconsistent?

I'm working with datasets from here http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32474 (with NCI_ADR_RES and OV:OVCAR_8 samples (3-3 samples)

> sessionInfo()

R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Hungarian_Hungary.1250 LC_CTYPE=Hungarian_Hungary.1250
[3] LC_MONETARY=Hungarian_Hungary.1250 LC_NUMERIC=C
[5] LC_TIME=Hungarian_Hungary.1250

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

other attached packages:
[1] pheatmap_0.7.7 affyQCReport_1.44.0
[3] simpleaffy_2.42.0 IDPmisc_1.1.17
[5] arrayQualityMetrics_3.22.1 Formula_1.2-0
[7] survival_2.37-7 lattice_0.20-29
[9] gridSVG_1.4-3 genefilter_1.48.1
[11] Cairo_1.5-6 affyPLM_1.42.0
[13] preprocessCore_1.28.0 gcrma_2.38.0
[15] affy_1.44.0 beadarray_2.16.0
[17] ggplot2_1.0.0 BBmisc_1.9
[19] Biobase_2.26.0 BiocGenerics_0.12.1
[21] BiocInstaller_1.16.1

loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 affyio_1.34.0 annotate_1.44.0
[4] AnnotationDbi_1.28.1 base64_1.1 BeadDataPackR_1.18.0
[7] Biostrings_2.34.1 checkmate_1.5.1 cluster_2.0.1
[10] colorspace_1.2-4 DBI_0.3.1 digest_0.6.8
[13] foreign_0.8-62 GenomeInfoDb_1.2.4 GenomicRanges_1.18.4
[16] gtable_0.1.2 Hmisc_3.15-0 hwriter_1.3.2
[19] illuminaio_0.8.0 IRanges_2.0.1 latticeExtra_0.6-26
[22] limma_3.22.4 MASS_7.3-37 munsell_0.4.2
[25] nnet_7.3-9 plyr_1.8.1 proto_0.3-10
[28] RColorBrewer_1.1-2 Rcpp_0.11.4 reshape2_1.4.1
[31] RJSONIO_1.3-0 rpart_4.1-9 RSQLite_1.0.0
[34] S4Vectors_0.4.0 scales_0.2.4 setRNG_2013.9-1
[37] stats4_3.1.2 stringr_0.6.2 SVGAnnotation_0.93-1
[40] tools_3.1.2 vsn_3.34.0 XML_3.98-1.1
[43] xtable_1.7-4 XVector_0.6.0 zlibbioc_1.12.0
>

Thank,

Anna

microarray affy cancer hgu133plus2 package • 1.9k views

ADD COMMENT • link updated 9.2 years ago by James W. MacDonald 65k • written 9.2 years ago by kanacska ▴ 10

score 0 · Answer 1 · 2015-02-17

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Entering edit mode

James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 3 hours ago

United States

You may have some files that got corrupted somehow, as I can process all the files for that GSE:

> getGEOSuppFiles("GSE32474")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE32nnn/GSE32474/suppl/
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  789M  100  789M    0     0  11.6M      0  0:01:08  0:01:08 --:--:-- 7539k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 12099  100 12099    0     0   7556      0  0:00:01  0:00:01 --:--:--  7557

> setwd("GSE32474/")
> untar("GSE32474_RAW.tar")

> library(affy)
> dat <- ReadAffy()
>

You might try downloading again to see if that helps. You could also try reading in each file separately, to see if it is just a particular file that is corrupted, and then just download that one.

ADD COMMENT • link 9.2 years ago James W. MacDonald 65k

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Entering edit mode

Hi James,

Thank you!

I will try that!

I didn't wright it in my first question that, is it a problem if I only downloaded the GSM files which have the data for my two cell line and not the whole GSE32474 .RAW fájl?

ADD REPLY • link 9.2 years ago kanacska ▴ 10

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Entering edit mode

Ah, I think the error is in your sNames vector:

> dat <- ReadAffy(filenames = dir(".","cel.gz$")[1:6], sampleNames = c(paste0("Sample",1:5), NA))
Error in value[[3L]](cond) : row names contain missing values
  AnnotatedDataFrame 'initialize' could not update varMetadata:
  perhaps pData and varMetadata are inconsistent?

So it looks like there is either an NA to begin with, or one or more of the sampleNames you are passing in are getting munged to NA by this code in AllButCelsForReadAffy():

if (length(sampleNames) != length(filenames)) {
        warning("sampleNames not same length as filenames. Using filenames as sampleNames instead\n")
        sampleNames <- sub("^/?([^/]*/)*", "", filenames)
    }

So you might want to just read in without specifying the sampleNames, and if you want to change after the fact you can do that then.

ADD REPLY • link 9.2 years ago James W. MacDonald 65k