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Forum: RNA Sequencing 03-05-2015, 12:38 PM
Replies: 155
Views: 59,875
Posted By Xi Wang
1) Zscore >0 is equivalent to log2(Fold_change) >...

1) Zscore >0 is equivalent to log2(Fold_change) > 0
2) negative Zscores, nagative log2(Fold_change), then expression in condition 1 < that in condition 2, thus up-regulated in condition 2.
Forum: RNA Sequencing 05-26-2014, 05:28 AM
Replies: 20
Views: 10,330
Posted By Xi Wang
You are right. Maybe you can decrease the...

You are right. Maybe you can decrease the permutation time to 250, or increase your samples size. If there are 6 samples per group, the random label assignment makes 924 combinations. It will not be...
Forum: RNA Sequencing 05-26-2014, 05:27 AM
Replies: 20
Views: 10,330
Posted By Xi Wang
Sorry that the current version of SeqGSEA cannot...

Sorry that the current version of SeqGSEA cannot work on less than 5 samples per group.

Xi
Forum: RNA Sequencing 05-13-2014, 11:32 AM
Replies: 20
Views: 10,330
Posted By Xi Wang
1) I suggestion you feed all genes to SeqGSEA,...

1) I suggestion you feed all genes to SeqGSEA, and SeqGSEA would apply itself filter to exclude unexpressed genes.
2) Sorry with the current version cannot.
Forum: RNA Sequencing 05-13-2014, 12:25 AM
Replies: 20
Views: 10,330
Posted By Xi Wang
A set of example data can be found by executing...

A set of example data can be found by executing the following command:
system.file("extdata", package="SeqGSEA", mustWork=TRUE)
Forum: RNA Sequencing 05-13-2014, 12:23 AM
Replies: 20
Views: 10,330
Posted By Xi Wang
I will try to move to DESeq2 in the future but at...

I will try to move to DESeq2 in the future but at present the most easy way to deal with this issue is just rerun DESeq analysis using the SeqGSEA pipeline. We have already provided one all-in...
Forum: RNA Sequencing 03-03-2014, 05:28 AM
Replies: 20
Views: 10,330
Posted By Xi Wang
Thanks for considering SeqGSEA. The gene...

Thanks for considering SeqGSEA.

The gene sets can be downloaded from http://www.broadinstitute.org/gsea/msigdb/index.jsp

Or in GMT format if you want to specify yourself...
Forum: Bioinformatics 10-01-2013, 07:44 AM
Replies: 3
Views: 2,277
Posted By Xi Wang
Hi Can you describe your problem in more details,...

Hi Can you describe your problem in more details, including information such as how your gene IDs look like and what kind of gene set data you have, and can you send them to me via email:...
Forum: RNA Sequencing 09-08-2013, 11:10 PM
Replies: 20
Views: 10,330
Posted By Xi Wang
Thanks for checking the latest version of SeqGSEA...

Thanks for checking the latest version of SeqGSEA :-)

You should also count reads on exons, and output the read counts per sample. As to the format, please refer to the files in the directory:
...
Forum: RNA Sequencing 07-02-2013, 11:26 PM
Replies: 20
Views: 10,330
Posted By Xi Wang
The package SeqGSEA started with R version 3.0.0....

The package SeqGSEA started with R version 3.0.0. Perhaps you need to install the latest release of R. If you are not happy with the latest R, and if you are based on Linux platform, you can download...
Forum: Academic/Non-Profit Jobs 05-08-2013, 04:26 PM
Replies: 0
Views: 2,655
Posted By Xi Wang
Bioinformatics Postdoc Open at the University of Newcastle, Australia

We are looking for a postdoctoral fellow to join our group in the School of Biomedical Sciences and Pharmacy, the University of Newcastle. Our group is led by Dr Murray Cairns, running the Molecular...
Forum: Bioinformatics 05-04-2013, 01:40 AM
Replies: 3
Views: 2,186
Posted By Xi Wang
Thanks for the info. I am afraid 2...

Thanks for the info.

I am afraid 2 replicates are too few for SeqGSEA, as its based on sample label permutation for statistical significance.

Regarding your questions, SeqGSEA doesn't require...
Forum: Bioinformatics 05-02-2013, 09:29 PM
Replies: 3
Views: 2,186
Posted By Xi Wang
Hi, If you haven't solved this out, I'd like to...

Hi, If you haven't solved this out, I'd like to suggest you try our newly developed R package SeqGSEA, which is available at http://bioconductor.org/packages/release/bioc/html/SeqGSEA.html.

It...
Forum: RNA Sequencing 04-28-2013, 04:18 AM
Replies: 20
Views: 10,330
Posted By Xi Wang
Thanks for your message. I have included an...

Thanks for your message. I have included an example in Section 6 in the package's vignette available at http://bioconductor.org/packages/release/bioc/vignettes/SeqGSEA/inst/doc/SeqGSEA.pdf

Any...
Forum: Bioinformatics 04-23-2013, 11:12 PM
Replies: 3
Views: 2,277
Posted By Xi Wang
Just in case some of you didn't see the original...

Just in case some of you didn't see the original post :-)
Forum: RNA Sequencing 04-15-2013, 04:43 PM
Replies: 20
Views: 10,330
Posted By Xi Wang
SeqGSEA: Gene Set Enrichment Analysis of RNA-Seq Data

I am glad to introduce to you guys a new Bioconductor package, SeqGSEA, developed by our group. The detailed description of this package is:

SeqGSEA: Gene set enrichment analysis of...
Forum: Bioinformatics 04-15-2013, 04:41 PM
Replies: 3
Views: 2,277
Posted By Xi Wang
SeqGSEA: Gene Set Enrichment Analysis of RNA-Seq Data

I am glad to introduce to you guys a new Bioconductor package, SeqGSEA, developed by our group. The detailed description of this package is:

SeqGSEA: Gene set enrichment analysis of...
Forum: Bioinformatics 08-22-2012, 09:20 PM
Replies: 2
Views: 2,139
Posted By Xi Wang
Anyone can help?

Anyone can help?
Forum: Bioinformatics 06-27-2012, 07:56 AM
Replies: 15
Views: 9,123
Posted By Xi Wang
Hi Nice to meet you here. ncRNA is a hot topic...

Hi Nice to meet you here. ncRNA is a hot topic but lots of questions to be answered. Hopefully, you and your collaborator can answer this question :-)
Forum: Bioinformatics 06-27-2012, 07:53 AM
Replies: 15
Views: 9,123
Posted By Xi Wang
In many gene annotation databases, miRNA host...

In many gene annotation databases, miRNA host genes are defined as ncRNAs. As miRNAs can be embedded in introns of coding RNAs, I think these corresponding pre-miRNAs can also be different...
Forum: Bioinformatics 06-24-2012, 11:54 PM
Replies: 15
Views: 9,123
Posted By Xi Wang
Thanks. Are you from biology background?

Thanks. Are you from biology background?
Forum: RNA Sequencing 06-14-2012, 08:56 PM
Replies: 155
Views: 59,875
Posted By Xi Wang
Thanks for your question. The q-values are...

Thanks for your question. The q-values are calculated by function in 'samr' package, and we didn't change anything regarding the calculation of q-values. You may have to add a small number (say 1e-6)...
Forum: Bioinformatics 05-24-2012, 10:10 PM
Replies: 513
Views: 199,848
Posted By Xi Wang
Seems its a bug of Bowtie2. Probably you may...

Seems its a bug of Bowtie2. Probably you may report it to the developers.
Forum: Bioinformatics 05-24-2012, 06:01 PM
Replies: 513
Views: 199,848
Posted By Xi Wang
It seems that it has nothing to do with M if a...

It seems that it has nothing to do with M if a read is not mappable. Because in this mode, "The search terminates when it can't find more distinct valid alignments, or when it finds M+1 distinct...
Forum: Bioinformatics 05-06-2012, 06:48 AM
Replies: 13
Views: 9,758
Posted By Xi Wang
Yes, the running time for "segment_juncs" dealing...

Yes, the running time for "segment_juncs" dealing with a large data set can be very slow. You may have a look at the logs folder, where up-to-date progress is recorded. I hadn't looked into this...
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