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Question: NA's returned for GEO GPL3921 platform probsets
1
gravatar for Zach Roe
15 months ago by
Zach Roe10
Zach Roe10 wrote:

Hi,

I am re-downloading a GSE Series I have worked with for several years, and suddenly encountered error in my code I have been using without issue for also several years.  As it turns out the probset information for the GPL3921 platform is not downloading properly.  I am not sure if this is GEOquery download issue or the GPL soft file on GEO is corrupt (it was last updated on the GEO website 8/12/16).

I have tried to download several times (deleting the cached copy each time), and either no probeset information is downloaded, OR a partial probset information is downloaded leaving the rest NA.

This gse has 2 datasets attached to it, there is no problem with the second gpl, GPL4685

Case #1: No probeset info downloaded, see featureData: none, and warning error

> gse50444 <- getGEO('gse50444', GSEMatrix = TRUE)

Download warning produced:

Warning message:
In readLines(con, 1) :
  incomplete final line found on '/var/folders/4z/w7_jy74n1nx7sf4hdcn4h4tm0000gn/T//RtmpWDrYrH/GPL3921.soft'

No featureData associated with Exression Set:

> gse50444.gpl3921 <- gse50444[[1]]
> gse50444.gpl3921
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22277 features, 13 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM1219374 GSM1219375 ... GSM1219390 (13 total)
  varLabels: title geo_accession ... data_row_count (35 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: GPL3921 

Case #2: No download warning error produced, but only partial probeset downloaded (different times produced different partial downloads:  e.g. the first 53 probes, the first 10 probes etc), NA's introduced for remainder.

> gse50444 <- getGEO('gse50444', GSEMatrix = TRUE)
> gse50444.gpl3921 <- gse50444[[1]]
> gse50444.gpl4685 <- gse50444[[2]]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22277 features, 13 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM1219374 GSM1219375 ... GSM1219390 (13 total)
  varLabels: title geo_accession ... data_row_count (35 total)
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... NA.22263 (22277 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL3921

​Partial information for probeset downloaded
​
> featureData(gse50444.gpl3921)$ID[1:50]
[1] 1007_s_at 1053_at   117_at    121_at    1255_g_at 1294_at   1316_at   1320_at
[9] 1405_i_at 1431_at   1438_at   1487_at   1494_f_at <NA>      <NA>      <NA>   
[17] <NA>      <NA>      <NA>      <NA>      <NA>      <NA>      <NA>      <NA>   
[25] <NA>      <NA>      <NA>      <NA>      <NA>      <NA>      <NA>      <NA>   
[33] <NA>      <NA>      <NA>      <NA>      <NA>      <NA>      <NA>      <NA>   
[41] <NA>      <NA>      <NA>      <NA>      <NA>      <NA>      <NA>      <NA>   
[49] <NA>      <NA>

> exprs(gse50444.gpl3921)[1:25, 1:5]
           GSM1219374  GSM1219375  GSM1219376  GSM1219377  GSM1219382
1007_s_at  0.41385892 -0.63996374 -1.73610412 -1.57517607 -1.07331220
1053_at   -0.12878988 -1.00403804 -0.73231870 -1.16391881 -0.77008163
117_at    -1.26070358  1.26937376  1.00263645  0.95988674  0.85146114
121_at     1.77211067  1.66987587 -0.98424704 -1.59976481 -0.50925136
1255_g_at  2.10582626  0.12738699 -0.12883987 -0.31430216  0.76752995
1294_at   -1.35346212 -1.54300280 -1.51740293 -0.78928326  0.08942978
1316_at    0.64331735  0.88807124  0.72578215  0.57944596 -2.87895589
1320_at   -2.48933703 -0.68146255  0.04693923 -1.29023574  1.42692626
1405_i_at -1.24342923 -0.98998659 -0.76558138 -0.89682371  1.56075510
1431_at    1.11565231  0.19878199  0.82711198  0.26595467  0.34545898
1438_at    1.39958352  1.15349628  1.25051712  1.27550538 -0.99547150
1487_at    0.07843472  0.85933824  1.45393915  1.96911334 -2.01832498
1494_f_at  0.46256203 -1.68187670  0.68478356  0.57685428  0.16596064
NA        -0.11693547  0.43283197 -1.72592572 -1.81656636  0.59357536
NA.1       2.11614697  2.09774366 -0.46119476 -0.67307001  0.17831501
NA.2      -0.87134590 -0.01708055 -2.50694865 -1.15106562 -0.04434486
NA.3      -0.40180877 -0.43061066 -0.81721768 -0.99795365 -0.25247241
NA.4       1.14204017 -0.75941455 -1.89897048 -1.57962924  1.43090640
NA.5       0.37910692  0.12075928 -0.05456004  0.97155238 -0.64881493
NA.6       1.43481442  0.10490435  2.01492490  1.28410018 -0.17900697
NA.7       1.43346276  0.52050705  1.46460961  1.89953704 -0.96485518
NA.8       1.78761277  0.91176840 -0.07419414  0.03137913  1.46269737
NA.9       0.58698465  0.78548994  1.77385158  1.52612317 -1.36141323
NA.10      0.98628179  0.81391549  1.72908608  1.69564966 -1.22285385
NA.11      0.03509782  0.43000220 -2.50945545 -1.18538264  0.38360561

Session Info is below.

Thank you.

 

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] HGNChelper_0.3.1     org.Hs.eg.db_3.3.0   AnnotationDbi_1.34.4 IRanges_2.6.1       
 [5] S4Vectors_0.10.2     lumi_2.24.0          mclust_5.2           limma_3.28.17       
 [9] affy_1.50.0          cluster_2.0.4        reshape_0.8.5        ggplot2_2.1.0       
[13] gplots_3.0.1         RColorBrewer_1.1-2   GEOquery_2.38.4      Biobase_2.32.0      
[17] BiocGenerics_0.18.0  BiocInstaller_1.22.3 gridExtra_2.2.1      dendextend_1.2.0    

 

 

ADD COMMENTlink modified 9 months ago • written 15 months ago by Zach Roe10
0
gravatar for Zach Roe
9 months ago by
Zach Roe10
Zach Roe10 wrote:

FYI, I received answer from GEO support thought to share that I have confirmed this was simply due to network error.

I rerun my code on a different day and did not encounter the problems anymore so it seems to be a specific network problem the day I was running my code.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Zach Roe10
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