getGEO Error: Duplicate identifiers for rows
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1
Entering edit mode
cg ▴ 10
@cg-14486
Last seen 7.0 years ago

Please Help!   Why does getGEO return "Error: Duplicate identifiers for rows​"?

How can this error be fixed?  This getGEO command was working fine for a week and then Stop working  without warning.

same error with  gep76275  <- getGEO(  "GSE76275")

same error with getGEO( "GSE31448" )

> source("http://www.bioconductor.org/biocLite.R")
> biocLite(pkgs=  c(  "Biobase", "IRanges", "AnnotationDbi", "GEOquery")   )
> library(Biobase)
> library(GEOquery)
> getwd()
> setwd("D:\\I_\\_Gene\\R\\desktopBrstC")
> getwd() 
> gc(verbose=T)
>  gep76275  <- GEOquery::getGEO(  "GSE76275", GSEMatrix = TRUE , destdir="D:\\I_\\_Gene\\R\\desktopBrstC")
Found 1 file(s)
GSE76275_series_matrix.txt.gz
Using locally cached version: D:\I_\_Gene\R\desktopBrstC/GSE76275_series_matrix.txt.gz
Error: Duplicate identifiers for rows (4506, 4771), (4508, 4773), (4510, 4775), (4511, 4776), (4512, 4777), (4513, 4778), (4514, 4779), (4515, 4780), (4516, 4781), (4518, 4783), (4524, 4789), (4525, 4790), (4526, 4791), (4528, 4793), (4532, 4797), (4533, 4798), (4535, 4800), (4538, 4803), (4274, 4539, 4804), (4275, 4540, 4805), (4541, 4806), (4544, 4809), (4549, 4814), (4550, 4815), (4556, 4821), (4572, 4837), (4308, 4573, 4838), (4574, 4839), (4311, 4576, 4841), (4577, 4842), (4580, 4845), (4317, 4582, 4847), (4594, 4859), (4595, 4860), (4334, 4599, 4864), (4335, 4600, 4865), (4612, 4877), (4350, 4615, 4880), (4351, 4616, 4881), (4352, 4617, 4882), (4353, 4618, 4883), (4354, 4619, 4884), (4622, 4887), (4361, 4626, 4891), (4631, 4896), (4655, 4920), (4656, 4921), (4668, 4933), (4405, 4670, 4935), (4408, 4673, 4938), (4674, 4939), (4675, 4940), (4682, 4947), (4683, 4948), (4686, 4951), (4693, 4958), (4694, 4959), (4696, 4961), (4432, 4697, 4962), (4438, 4703, 4968), (3644, 3909, 4174,

> gep76275  <- GEOquery::getGEO(  "GSE76275")
Found 1 file(s)
GSE76275_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76275/matrix/GSE76275_series_matrix.txt.gz'
Content type 'application/x-gzip' length 78267950 bytes (74.6 MB)
downloaded 74.6 MB
Error: Duplicate identifiers for rows (4506, 4771), (4508, 4773), (4510, 4775), (4511, 4776), (4512, 4777), (4513, 4778), (4514, 4779), (4515, 4780), (4516, 4781), (4518, 4783), (4524, 4789), (4525, 4790), (4526, 4791), (4528, 4793), (4532, 4797), (4533, 4798), (4535, 4800), (4538, 4803), (4274, 4539, 4804), (4275, 4540, 4805), (4541, 4806), (4544, 4809), (4549, 4814), (4550, 4815), (4556, 4821), (4572, 4837), (4308, 4573, 4838), (4574, 4839), (4311, 4576, 4841), (4577, 4842), (4580, 4845), (4317, 4582, 4847), (4594, 4859), (4595, 4860), (4334, 4599, 4864), (4335, 4600, 4865), (4612, 4877), (4350, 4615, 4880), (4351, 4616, 4881), (4352, 4617, 4882), (4353, 4618, 4883), (4354, 4619, 4884), (4622, 4887), (4361, 4626, 4891), (4631, 4896), (4655, 4920), (4656, 4921), (4668, 4933), (4405, 4670, 4935), (4408, 4673, 4938), (4674, 4939), (4675, 4940), (4682, 4947), (4683, 4948), (4686, 4951), (4693, 4958), (4694, 4959), (4696, 4961), (4432, 4697, 4962), (4438, 4703, 4968), (3644, 3909, 4174,


> gep76275  <- getGEO(  "GSE76275")
Found 1 file(s)
GSE76275_series_matrix.txt.gz
Using locally cached version: C:\Users\cangincc\AppData\Local\Temp\RtmpCm5HRI/GSE76275_series_matrix.txt.gz
Error: Duplicate identifiers for rows (4506, 4771), (4508, 4773), (4510, 4775), (4511, 4776), (4512, 4777), (4513, 4778), (4514, 4779), (4515, 4780), (4516, 4781), (4518, 4783), (4524, 4789), (4525, 4790), (4526, 4791), (4528, 4793), (4532, 4797), (4533, 4798), (4535, 4800), (4538, 4803), (4274, 4539, 4804), (4275, 4540, 4805), (4541, 4806), (4544, 4809), (4549, 4814), (4550, 4815), (4556, 4821), (4572, 4837), (4308, 4573, 4838), (4574, 4839), (4311, 4576, 4841), (4577, 4842), (4580, 4845), (4317, 4582, 4847), (4594, 4859), (4595, 4860), (4334, 4599, 4864), (4335, 4600, 4865), (4612, 4877), (4350, 4615, 4880), (4351, 4616, 4881), (4352, 4617, 4882), (4353, 4618, 4883), (4354, 4619, 4884), (4622, 4887), (4361, 4626, 4891), (4631, 4896), (4655, 4920), (4656, 4921), (4668, 4933), (4405, 4670, 4935), (4408, 4673, 4938), (4674, 4939), (4675, 4940), (4682, 4947), (4683, 4948), (4686, 4951), (4693, 4958), (4694, 4959), (4696, 4961), (4432, 4697, 4962), (4438, 4703, 4968), (3644, 3909, 4174,

>  gep76275 <- make.names(  (getGEO("GSE76275"))[,1], unique=TRUE)
Found 1 file(s)
GSE76275_series_matrix.txt.gz
Using locally cached version: C:\Users\cangincc\AppData\Local\Temp\RtmpCm5HRI/GSE76275_series_matrix.txt.gz
Error: Duplicate identifiers for rows (4506, 4771), (4508, 4773), (4510, 4775), (4511, 4776), (4512, 4777), (4513, 4778), (4514, 4779), (4515, 4780), (4516, 4781), (4518, 4783), (4524, 4789), (4525, 4790), (4526, 4791), (4528, 4793), (4532, 4797), (4533, 4798), (4535, 4800), (4538, 4803), (4274, 4539, 4804), (4275, 4540, 4805), (4541, 4806), (4544, 4809), (4549, 4814), (4550, 4815), (4556, 4821), (4572, 4837), (4308, 4573, 4838), (4574, 4839), (4311, 4576, 4841), (4577, 4842), (4580, 4845), (4317, 4582, 4847), (4594, 4859), (4595, 4860), (4334, 4599, 4864), (4335, 4600, 4865), (4612, 4877), (4350, 4615, 4880), (4351, 4616, 4881), (4352, 4617, 4882), (4353, 4618, 4883), (4354, 4619, 4884), (4622, 4887), (4361, 4626, 4891), (4631, 4896), (4655, 4920), (4656, 4921), (4668, 4933), (4405, 4670, 4935), (4408, 4673, 4938), (4674, 4939), (4675, 4940), (4682, 4947), (4683, 4948), (4686, 4951), (4693, 4958), (4694, 4959), (4696, 4961), (4432, 4697, 4962), (4438, 4703, 4968), (3644, 3909, 4174,

 

 

getGEO • 1.3k views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 48 minutes ago
United States

You are reading in locally cached versions, all of which seem to be borked. Have you tried deleting those and re-downloading?

> gep76275  <- getGEO(  "GSE76275")
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76275/matrix/
OK
Found 1 file(s)
GSE76275_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76275/matrix/GSE76275_series_matrix.txt.gz'
Content type 'application/x-gzip' length 78267950 bytes (74.6 MB)
downloaded 74.6 MB

File stored at:
C:\Users\Public\Documents\Wondershare\CreatorTemp\Rtmp2fu9NG/GPL570.soft
Warning message:
In read.table(file = file, header = header, sep = sep, quote = quote,  :
  not all columns named in 'colClasses' exist
> gep76275[[1]]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 265 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM1974566 GSM1974567 ... GSM1978949 (265 total)
  varLabels: title geo_accession ... data_row_count (50 total)
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL570
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