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Old 09-10-2014, 06:15 PM   #1
tinguzman
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Location: Philippines

Join Date: Aug 2014
Posts: 13
Default loading custom annotation on topgo

Hi,

I'm stuck on loading my customize annotation on topgo using R. I have a .txt file containing list of genes and their GO Ids.

Genes Gene ontology IDs
c10020_g1 GO:0047021; GO:0019369; GO:0004090; GO:0019371; GO:0005829; GO:0017144; GO:0030855; GO:0070062; GO:0055114; GO:0016655; GO:0050221; GO:0044281; GO:0042373
c10035_g1 GO:0005524; GO:0016887; GO:0005929; GO:0005737; GO:0030286; GO:0005874; GO:0003777; GO:0007018; GO:0005515
c10052_g1 GO:0005737; GO:0016021; GO:0008168

When I tried to upload this to topgo, here's the error message:

> geneID2GO <- readMappings(file = ".../Htub_gene_list_complete_annots.txt", sep="\t")

Error in `[.data.frame`(a, , 2) : undefined columns selected
In addition: Warning messages:
1: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 1 appears to contain embedded nulls
2: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 3 appears to contain embedded nulls
3: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 4 appears to contain embedded nulls
4: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 5 appears to contain embedded nulls
5: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
embedded nul(s) found in input


I can't figure out what is wrong? Can somebody help me. thanks!


Best,
Christine
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Old 09-10-2014, 06:32 PM   #2
tinguzman
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Location: Philippines

Join Date: Aug 2014
Posts: 13
Default

Hi again,

I loaded the custom annotation successfully, however when I tried to load my list of DEGs with Pvalues, I again encountered an error


DEGs PValue
c33534_g1 2.61E-239
c52364_g1 3.60E-211
c57190_g1 2.24E-178
c56306_g1 2.17E-175
c52707_g1 7.61E-182
c49291_g10 3.08E-154
c53016_g2 1.03E-169

> AvsB <- read.csv("/Users/mmbl/Desktop/Htub_edgeR_filtered_AvsB.csv", header = TRUE)
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
duplicate 'row.names' are not allowed
In addition: Warning messages:
1: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 1 appears to contain embedded nulls
2: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 2 appears to contain embedded nulls
3: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 4 appears to contain embedded nulls
4: In read.table(file = file, header = header, sep = sep, quote = quote, :
line 5 appears to contain embedded nulls
5: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
embedded nul(s) found in input

It says that i have duplicates in row.names, but Im sure that the genes are all unique.

thanks,
christine
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Old 04-29-2015, 03:45 AM   #3
ebioman
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Location: Switzerland

Join Date: Aug 2013
Posts: 41
Default Help solve problems for the next ones

Hello tinguzman
Since you figured out by yourself how to fix the first problem would you mind sharing
your solution ? I just encountered the same issue and was a little bit disappointing that
you managed to fix it but you don't tell us how.
cheers
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