Question

error reading GSE file

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Reema Singh ▴ 570

@reema-singh-4373

Last seen 11.2 years ago

Dear all I am trying to read a GSE file in R using GEOquery package but i am getting following error.Kindly tell me why i am getting this error. I have tried to find out on google. But no luck... u <- getGEO(filename="GSE1106_family.soft",GSEMatrix=TRUE) Parsing.... Found 22 entities... GPL199 (1 of 22 entities) GSM18235 (2 of 22 entities) GSM18236 (3 of 22 entities) Error in substr(x, start = matches + patlen, stop = 1e+07) : invalid multibyte string at '<92>s pre' In addition: There were 20 warnings (use warnings() to see them) Regards~ Reema Singh [[alternative HTML version deleted]]

GEOquery GEOquery • 1.9k views

ADD COMMENT • link updated 10.9 years ago by acd13 • 0 • written 14.3 years ago by Reema Singh ▴ 570

score 0 · Answer 1 · 2011-07-26

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Sean Davis 21k

@sean-davis-490

Last seen 8 months ago

United States

On Tue, Jul 26, 2011 at 6:38 AM, Reema Singh <reema28sep at="" gmail.com=""> wrote: > Dear all > > I am trying to read a GSE file in R using GEOquery package but i am getting > following error.Kindly tell me why i am getting this error. I have tried to > find out on google. But no luck... > > u <- getGEO(filename="GSE1106_family.soft",GSEMatrix=TRUE) > Parsing.... > Found 22 entities... > GPL199 (1 of 22 entities) > GSM18235 (2 of 22 entities) > GSM18236 (3 of 22 entities) > Error in substr(x, start = matches + patlen, stop = 1e+07) : > ?invalid multibyte string at '<92>s pre' Hi, Reema. This is caused by an invalid character in the data from NCBI. I have contacted them to fix the problem. In the meantime, you can try: u = getGEO('GSE1106') This will grab the GSEMatrix file which is apparently unaffected. Sean

ADD COMMENT • link 14.3 years ago Sean Davis 21k

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On Tue, Jul 26, 2011 at 8:39 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Tue, Jul 26, 2011 at 6:38 AM, Reema Singh <reema28sep at="" gmail.com=""> wrote: >> Dear all >> >> I am trying to read a GSE file in R using GEOquery package but i am getting >> following error.Kindly tell me why i am getting this error. I have tried to >> find out on google. But no luck... >> >> u <- getGEO(filename="GSE1106_family.soft",GSEMatrix=TRUE) >> Parsing.... >> Found 22 entities... >> GPL199 (1 of 22 entities) >> GSM18235 (2 of 22 entities) >> GSM18236 (3 of 22 entities) >> Error in substr(x, start = matches + patlen, stop = 1e+07) : >> ?invalid multibyte string at '<92>s pre' > > Hi, Reema. > > This is caused by an invalid character in the data from NCBI. ?I have > contacted them to fix the problem. One has to love the GEO staff. They've already fixed the problem. Thanks for the report, Reema. Sean > In the meantime, you can try: > > u = getGEO('GSE1106') > > This will grab the GSEMatrix file which is apparently unaffected. > > Sean >

ADD REPLY • link 14.3 years ago Sean Davis 21k

score 0 · Answer 2 · 2014-12-30

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acd13 • 0

@acd13-7209

Last seen 10.9 years ago

United States

Sorry to pick up an old thread here, but I'm having the same issue, and also unable to find much of an answer after some searching.

Thanks for any and all help!

I'm running the command below

getGEO('GSE3118')

In the following setting

> sessionInfo()

R version 3.1.2 (2014-10-31)
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] parallel stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] affy_1.44.0 ArrayExpress_1.26.0 GEOquery_2.32.0
[4] Biobase_2.26.0 BiocGenerics_0.12.0 RMySQL_0.9-3
[7] DBI_0.3.1

loaded via a namespace (and not attached):
[1] affyio_1.34.0 BiocInstaller_1.16.1 limma_3.22.1
[4] preprocessCore_1.28.0 RCurl_1.95-4.3 XML_3.98-1.1
[7] zlibbioc_1.12.0

ADD COMMENT • link 10.9 years ago acd13 • 0

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You will need to give us more than that to go on. This works for me:

> geo <- getGEO('GSE3118')
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE3nnn/GSE3118/matrix/
Found 1 file(s)
GSE3118_series_matrix.txt.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  150k  100  150k    0     0  98938      0  0:00:01  0:00:01 --:--:-- 98890
File stored at:
/data3/tmp/RtmpC8WWiS/GPL2750.soft
> geo[[1]]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 36541 features, 3 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM69721 GSM69722 GSM69723
  varLabels: title geo_accession ... data_row_count (32 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: GPL2750
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-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] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] GEOquery_2.32.0     Biobase_2.26.0      BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6   RCurl_1.95-4.5 XML_3.98-1.1

ADD REPLY • link 10.9 years ago James W. MacDonald 68k