Question: Error in ReadAffy command
0
gravatar for 786
3.3 years ago by
78650
78650 wrote:

Hi I'm using R and facing same error in ReadAffy. Can u please tell me about this Ihave downloaded the complete file but still it gives me error. Can anyone let me know about it please it will be very helpful.. I'm working on GSE42902

> Study1 = "GSE42902"
> Gse42902dat = getGEO('GSE42902')
Found 1 file(s)
GSE42902_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/GSE42902/GSE42902_series_matrix.txt.gz'
ftp data connection made, file length 541891 bytes
opened URL
downloaded 529 Kb

File stored:
> filePaths=getGEOSuppFiles("GSE42902")
[1] "ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE42902/"
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE42902//GSE42902_RAW.tar'
ftp data connection made, file length 385873920 bytes
opened URL
downloaded 368.0 Mb

trying URL 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE42902//filelist.txt'
ftp data connection made, file length 1166 bytes
opened URL
downloaded 1166 bytes

> tarfile <- grep("\\.tar$", rownames(filePaths), value = TRUE) 
> untar(tarfile, exdir="GSE55650") 
> untar(tarfile, exdir="GSE42902") 
> celFiles <- unlist(list.files("GSE42902", pattern = "\\.CEL.gz", full.names = TRUE))

Error:

> gse42902preset = ReadAffy(filenames = celFiles) 
Error: cannot allocate vector of size 800.0 Mb
In addition: Warning messages:
1: In `colnames<-`(`*tmp*`, value = c("GSM1053073_S0608F0055a.CEL.gz",  :
  Reached total allocation of 1535Mb: see help(memory.size)
2: In `colnames<-`(`*tmp*`, value = c("GSM1053073_S0608F0055a.CEL.gz",  :
  Reached total allocation of 1535Mb: see help(memory.size)
3: In `colnames<-`(`*tmp*`, value = c("GSM1053073_S0608F0055a.CEL.gz",  :
  Reached total allocation of 1535Mb: see help(memory.size)
4: In `colnames<-`(`*tmp*`, value = c("GSM1053073_S0608F0055a.CEL.gz",  :

Please help me out I'll be very thankful. Reached total allocation of 1535Mb: see help(memory.size)

limma readaffy R • 1.1k views
ADD COMMENTlink modified 3.3 years ago by WouterDeCoster40k • written 3.3 years ago by 78650

Are you using 32-bit R?

ADD REPLYlink written 3.3 years ago by genomax70k

yes I'm using 32-bit R

ADD REPLYlink written 3.3 years ago by 78650
0
gravatar for WouterDeCoster
3.3 years ago by
Belgium
WouterDeCoster40k wrote:

Either your machine has not enough memory available, or the amount of memory that can be used by a user is too much restricted. On what kind of machine are you working?

ADD COMMENTlink written 3.3 years ago by WouterDeCoster40k

I'm using Hp Laptop..I'm working on this Platform

 [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]

Is there any problem with script?

ADD REPLYlink written 3.3 years ago by 78650
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