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,