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Search: Posts Made By: wmseq
Forum: Bioinformatics 05-27-2015, 07:26 AM
Replies: 2
Views: 759
Posted By wmseq
nepossiver, Thank you very much for your...

nepossiver,

Thank you very much for your advice!!!

Then, could I follow the protocol and analyze the DE genes with replicates?
Forum: Bioinformatics 05-27-2015, 06:56 AM
Replies: 2
Views: 759
Posted By wmseq
Question Does analysis of DE genes with Trinity need replicates?

I'd like to use Trinity to analyze DG genes of a non-model animal. According to the protocol for reference generation and analysis with Trinity on Nat Protoc. 2013, it seems that the analysis didn't...
Forum: Bioinformatics 02-21-2014, 08:25 AM
Replies: 1
Views: 2,722
Posted By wmseq
Can edgeR CPM be used like FPKM to represent a gene expression level in a figure?

Hi, every one,
I'd like drawing a figure like the following one:
...
Forum: Bioinformatics 12-12-2013, 11:13 AM
Replies: 14
Views: 5,350
Posted By wmseq
Hi bigmw, As to “Start tag expected, '<' not...

Hi bigmw,
As to “Start tag expected, '<' not found”, although I am not sure where it was from during my analysis session, I suspect the creation of exp.fc file. As you know, this file is created...
Forum: Bioinformatics 12-11-2013, 11:05 AM
Replies: 14
Views: 5,350
Posted By wmseq
Thank you very much, bigmw!! Maybe, You could...

Thank you very much, bigmw!!
Maybe, You could remember my questions on 12-09-2013:
> pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview(gene.data = exp.fc, pathway.id = pid, species...
Forum: Bioinformatics 12-10-2013, 06:46 AM
Replies: 14
Views: 5,350
Posted By wmseq
Hi bigmw, As you know, I used beebase gene IDs...

Hi bigmw,
As you know, I used beebase gene IDs at the beginning to do pathway analysis. With your help, I changed those IDs to Entrez Gene IDs, and do the analysis in R as follows:

> degene_data...
Forum: Bioinformatics 12-09-2013, 07:34 AM
Replies: 14
Views: 5,350
Posted By wmseq
Hi bigmw, After I run the command for pathway...

Hi bigmw,
After I run the command for pathway analysis, I got a weird information as follows:

> pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview(gene.data = exp.fc, pathway.id = pid,...
Forum: Bioinformatics 12-07-2013, 05:46 AM
Replies: 14
Views: 5,350
Posted By wmseq
bigmw, Sorry about the tittle. I have tried to...

bigmw,
Sorry about the tittle. I have tried to change it, but I don't know why I could not change it successfully, because the change can not be seen as the thread tittle outside.
Forum: Bioinformatics 12-06-2013, 06:02 AM
Replies: 14
Views: 5,350
Posted By wmseq
Hi bigmw, I am sorry to ask you two more...

Hi bigmw,
I am sorry to ask you two more questions based on your answer.
I did my pathway analysis according to the protocol on the paper,
“RNA-Seq Data Pathway and Gene-set Analysis Workflow”. ...
Forum: Bioinformatics 12-04-2013, 08:07 AM
Replies: 14
Views: 5,350
Posted By wmseq
Just want it to be seen now.

Just want it to be seen now.
Forum: Bioinformatics 12-03-2013, 06:51 AM
Replies: 14
Views: 5,350
Posted By wmseq
Does the gene set size for metabolism affect pathway identification by gage/pathview?

Hi bigmw,
With your kind help, I have finished pathway analysis of signal transduction and fond two disturbed pathways. But I met problem with metabolism pathway analysis, because I could not find...
Forum: Bioinformatics 12-02-2013, 09:50 AM
Replies: 1
Views: 1,306
Posted By wmseq
problem with extracting special gene sets from kegg gene sets for gage

Hi bigmw,
With your help, I have downloaded the whole pathway gene sets for honey bees from Kegg successfully. However, when I tried to extract the signaling/metabolic pathway using the command ...
Forum: Bioinformatics 11-27-2013, 07:43 AM
Replies: 7
Views: 2,663
Posted By wmseq
Thanks a lot, bigmw! I will consult a computer...

Thanks a lot, bigmw!
I will consult a computer guy to do it.
Forum: Bioinformatics 11-26-2013, 12:48 PM
Replies: 7
Views: 2,663
Posted By wmseq
Hi bigmw, I have solved the problem. It was...

Hi bigmw,
I have solved the problem. It was because some files in a local directory could not be updated automatically, so that they have to be removed by hand, and than update R.

Now, I can find...
Forum: Bioinformatics 11-26-2013, 12:28 AM
Replies: 7
Views: 2,663
Posted By wmseq
Thanks, bigmw! I am sure I installed it from...

Thanks, bigmw!
I am sure I installed it from Bioconducto 2.13.
The commands I used are as follows:
source("http://bioconductor.org/biocLite.R")
biocLite("gage")
Forum: Bioinformatics 11-25-2013, 08:30 AM
Replies: 7
Views: 2,663
Posted By wmseq
Why could I not find "kegg.gsets" function in gage package?

Hi bigmw,
I could not find the function of "kegg.gsets" in gage package. Do you have any idea about it?
Was it because I used version 2. 12.0 instead of 2.11.3?
> library(gage)
> ?kegg.gsets
No...
Forum: Bioinformatics 11-25-2013, 06:26 AM
Replies: 11
Views: 3,499
Posted By wmseq
Hi bigmw, Why I could not find the function of...

Hi bigmw,
Why I could not find the function of "kegg.gsets" in gage package?

> library(gage)
> ?kegg.gsets
No documentation for ‘kegg.gsets’ in specified packages and libraries:
you could try...
Forum: Bioinformatics 11-23-2013, 02:06 AM
Replies: 11
Views: 3,499
Posted By wmseq
Thank you vary much, bigmw! Another question: ...

Thank you vary much, bigmw!
Another question:
If I'd like to use all the pathways or a special one, how to extract them or it for my analysis?
Forum: Bioinformatics 11-22-2013, 03:12 PM
Replies: 11
Views: 3,499
Posted By wmseq
What genesets can I use for pathway analysis of honeybee seq data?

bigmw,
Thanks a lot for your quick answer!
I have solved the problem, because GeneID is in column2.

>names(edger.fc) = test$GeneID
> head(exp.fc)
409677 100576979 100577819 552035 413550...
Forum: Bioinformatics 11-22-2013, 08:57 AM
Replies: 3
Views: 1,917
Posted By wmseq
Why could I not load gage?

Hi every one,
After I started R again and seted the same directory as last time, why I could not load gage with command---library(gage) and got the following information:

> library(gage)
Error...
Forum: Bioinformatics 11-18-2013, 06:20 AM
Replies: 6
Views: 1,844
Posted By wmseq
Thank you very much, bigmw! I will do it as you...

Thank you very much, bigmw!
I will do it as you advised.
Forum: Bioinformatics 11-16-2013, 06:45 AM
Replies: 6
Views: 1,844
Posted By wmseq
Hi bigmw, The IDs are genbank accession...

Hi bigmw,
The IDs are genbank accession numbers. Now the problem is that I am working on honey bee, a non model animal, and how can I convert these IDs to Entrez Gene IDs?
Thanks a lot!!
Forum: Bioinformatics 11-15-2013, 02:50 PM
Replies: 6
Views: 1,844
Posted By wmseq
4Hi bigmw, Thank you very much for your kind...

4Hi bigmw,
Thank you very much for your kind help!
I am at home, I could not give you the first few rows of exp.fc.

I could not remember the file name containing the gene IDs and FCs extracted...
Forum: Bioinformatics 11-15-2013, 12:43 PM
Replies: 6
Views: 1,844
Posted By wmseq
what is wrong with the gage?

Hi every one,
Wen I run the following command, I got the error information as follows:

> fc.kegg.p <- gage(exp.fc, gsets = kegg.gs, ref = NULL, samp = NULL)
Error in if (is.na(spval[i])) tmp[i]...
Forum: Bioinformatics 11-15-2013, 09:59 AM
Replies: 3
Views: 1,041
Posted By wmseq
Hi, GenoMax, I found the paragraph on jointing...

Hi, GenoMax,
I found the paragraph on jointing workflows with edge R. Thans!
Showing results 1 to 25 of 71

 


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