User: EagleEye
EagleEye • 5.0k
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Investigating field of biology by applying logics of computer science, statistics and mathematics.
Posts by EagleEye
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1.2k
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... please report the error message ...
written 3 days ago by
EagleEye • 5.0k
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120
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Comment:
C: edgeR RPKM Values
... Yes because your code is wrong.
Example:
rpkm<-rpkm(d,gene.data)
’gene.data’ has extra column of gene names in the first column. It just needs gene length colum. Try this in your above code, it might work.
rpkm<-rpkm(d$counts,gene.data[,2])
Else below mentioned complete sample c ...
written 9 days ago by
EagleEye • 5.0k
0
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0
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120
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0
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Comment:
C: edgeR RPKM Values
... group <- c(rep("Sample1",2),rep("Sample1",2))
Why do you have same sample names ('Sample1') for both group. I assume it is,
group <- c(rep("Sample1",2),rep("Sample2",2))
Sample Code:
data_raw <- read.table("counts.txt", header = T, sep='\t', row.names=1) # Assumed i ...
written 15 days ago by
EagleEye • 5.0k
0
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1
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183
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1
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... When you have doubt verify the results with other tools available for gene enrichment analysis. ...
written 18 days ago by
EagleEye • 5.0k
1
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2
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149
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2
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... **2. Background Selection (findMotifs.pl/findMotifsGenome.pl)**
If the background sequences were not explicitly defined, HOMER will automatically select them for you. If you are using genomic positions, sequences will be randomly selected from the genome, matched for GC% content (to make GC norma ...
written 21 days ago by
EagleEye • 5.0k
2
votes
2
answers
149
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2
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... Try Homer, http://homer.ucsd.edu/homer/motif/ ...
written 22 days ago by
EagleEye • 5.0k
0
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5
answers
5.9k
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5
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Comment:
C: Clinical Survival data of TCGA
... The link I have mentioned above will work. ...
written 4 weeks ago by
EagleEye • 5.0k
1
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1
answer
15k
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1
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... HI,
I have a list of 54000 gene-ids I want to annotate all the genes. Is there any other R package or command-line software that I can use?
**Answer:** Make this as separate post/question on Biostars. You will get quick help. ...
written 8 weeks ago by
EagleEye • 5.0k
0
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1
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15k
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1
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... Hi,
In GeneSCF you can only use Gene Symbols ([Example][1]) or Entrez GeneIDs ([Example][2]) as input. And the reason for the error you mentioned is because your input gene list does not match with the database consists of only Gene symbols and Entrez IDs ([Check reported issue][3]).
It is also cl ...
written 8 weeks ago by
EagleEye • 5.0k
0
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1
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15k
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1
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... Hi,
COMMAND-: ./prepare_database -db=GO -org=goa_human ERROR-: rm: cannot remove '/home/ibab/software/geneSCF-master-source-v1.1-p2/class/lib/db/gene_info_limit.gz': No such file or directory
**Answer:** Do not worry about this error. When it is not found, GeneSCF can download the database.
ERROR ...
written 8 weeks ago by
EagleEye • 5.0k
Latest awards to EagleEye
Popular Question
17 days ago,
created a question with more than 1,000 views.
For New article on TCGA data & useful resource: Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For New article on TCGA data & useful resource: Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: How to check the type of identifier from ensembl?
Good Answer
4 months ago,
created an answer that was upvoted at least 5 times.
For A: Something better than GSEA?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For RNA-seq differential expression analysis, which aligner to choose between BWA/tophat/Bowtie?
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: How to check the type of identifier from ensembl?
Appreciated
7 months ago,
created a post with more than 5 votes.
For A: How to check the type of identifier from ensembl?
Epic Question
8 months ago,
created a question with more than 10,000 views.
For Gene Set Clustering based on Functional annotation (GeneSCF)
Scholar
8 months ago,
created an answer that has been accepted.
For A: How to interpret the result of GO analysis using Ontologizer ?
Scholar
8 months ago,
created an answer that has been accepted.
For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: How to look up GO terms in BioMart using GI ID or Accession ID
Scholar
8 months ago,
created an answer that has been accepted.
For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Scholar
9 months ago,
created an answer that has been accepted.
For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Appreciated
10 months ago,
created a post with more than 5 votes.
For A: How to check the type of identifier from ensembl?
Appreciated
10 months ago,
created a post with more than 5 votes.
For A: How to check the type of identifier from ensembl?
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Clinical Survival data of TCGA
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Clinical Survival data of TCGA
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Clinical Survival data of TCGA
Good Answer
11 months ago,
created an answer that was upvoted at least 5 times.
For A: Something better than GSEA?
Scholar
11 months ago,
created an answer that has been accepted.
For A: How to interpret the result of GO analysis using Ontologizer ?
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