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Forum: Bioinformatics 09-24-2015, 05:21 PM
Replies: 92
Views: 38,233
Posted By bigmw
theoretically, you can. You need to derive GO...

theoretically, you can. You need to derive GO annotation for the genes of this species using tools like blast2go. Then generate GO gene set data like the ones used in gage tutorial. You need to use R...
Forum: Bioinformatics 08-28-2015, 06:06 AM
Replies: 92
Views: 38,233
Posted By bigmw
Bobby, Heatmaps from sigGeneSet function show...

Bobby,
Heatmaps from sigGeneSet function show the perturbations of whole gene sets or pathways (in experiment samples vs controls). It is only meaningful for exmperiment samples, you donít really...
Forum: Bioinformatics 09-13-2014, 11:00 AM
Replies: 92
Views: 38,233
Posted By bigmw
GAGE accepts log fold changes or other test...

GAGE accepts log fold changes or other test statistics from differential expression analysis. Yes, you need to set ref = NULL and samp = NULL in gage function when differential expression analysis is...
Forum: Bioinformatics 07-18-2014, 06:50 AM
Replies: 92
Views: 38,233
Posted By bigmw
Obviously, no pathways has q-val <0.1. this is...

Obviously, no pathways has q-val <0.1. this is still common due to the sample size, noise level etc in your data. You may do either one or both of the following:
-increase the q-val cutoff,...
Forum: Bioinformatics 07-17-2014, 10:29 AM
Replies: 92
Views: 38,233
Posted By bigmw
This is normal. Different analysis procedures...

This is normal. Different analysis procedures give you different p-values, although you can still see lot of consistency between the them (the top hits or order of significant pathways). We expect...
Forum: Bioinformatics 07-16-2014, 01:35 PM
Replies: 92
Views: 38,233
Posted By bigmw
You are right. In the demo examples GAGE takes...

You are right. In the demo examples GAGE takes fold changes, not the p-values as input.
GAGE works with fold change (default), t-stats and other types of statistics, please check the GAGE paper and...
Forum: Bioinformatics 07-16-2014, 09:26 AM
Replies: 92
Views: 38,233
Posted By bigmw
eg2id and id2eg are the pair of functions for ID...

eg2id and id2eg are the pair of functions for ID mapping from and to Entrez Genes. For info:
?eg2id
Forum: Bioinformatics 07-16-2014, 09:24 AM
Replies: 92
Views: 38,233
Posted By bigmw
GAGE and other methods (GSEA etc) require all...

GAGE and other methods (GSEA etc) require all genes included. This way GAGE test gene perturbations within pathways against the background of all genes. You selected a list of differentially...
Forum: Bioinformatics 07-15-2014, 05:09 PM
Replies: 92
Views: 38,233
Posted By bigmw
BTW, has a separate tutorial on data preparation,...

BTW, has a separate tutorial on data preparation, you can check Section 5 -- gene or transcript ID conversion:
http://www.bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/dataPrep.pdf
Forum: Bioinformatics 07-15-2014, 12:49 PM
Replies: 92
Views: 38,233
Posted By bigmw
The pathview package provides two functions:...

The pathview package provides two functions: eg2id and id2eg, for ID mapping/conversion for major research species. For details:
?pathview::eg2id

BTW, I would suggest you to convert your data ID...
Forum: Bioinformatics 07-10-2014, 06:05 AM
Replies: 92
Views: 38,233
Posted By bigmw
Just checked the source code for sigGeneSet and...

Just checked the source code for sigGeneSet and internal functions gs.heatmap. there seems to be a potential conflict in argument margins indeed. Will have the problem fixed. you can check the...
Forum: Bioinformatics 07-09-2014, 09:45 AM
Replies: 92
Views: 38,233
Posted By bigmw
This is the latest version. Do you still get the...

This is the latest version. Do you still get the problem?
Forum: Bioinformatics 07-07-2014, 08:54 AM
Replies: 92
Views: 38,233
Posted By bigmw
You may want to check the version of the gage...

You may want to check the version of the gage package you are running, which can be seen by:
sessionInfo()
Forum: Bioinformatics 04-07-2014, 12:10 PM
Replies: 92
Views: 38,233
Posted By bigmw
Thanks for the good words on GAGE. Let us know if...

Thanks for the good words on GAGE. Let us know if you have more comments/questions.
Forum: Bioinformatics 03-26-2014, 08:15 AM
Replies: 92
Views: 38,233
Posted By bigmw
Having that said, you can always do GAGE (or...

Having that said, you can always do GAGE (or other pathway analysis) on absolute expression levels. GAGE does work on single sample or condition (single-column matrices or vectors). But very likely,...
Forum: Bioinformatics 03-25-2014, 06:14 PM
Replies: 92
Views: 38,233
Posted By bigmw
In pathway analysis or gene set analysis, you may...

In pathway analysis or gene set analysis, you may still use absolute expression levels rather than relative expression levels. However, two things make absolute expression analyses less desirable.
...
Forum: Bioinformatics 03-23-2014, 02:15 PM
Replies: 92
Views: 38,233
Posted By bigmw
Forgot that sigGeneSet function has been updated...

Forgot that sigGeneSet function has been updated to give users more control on the margin and font size. sigGeneSet calls a internal function heatmap2 to generate the heatmaps. So check the argument...
Forum: Bioinformatics 03-22-2014, 10:17 AM
Replies: 92
Views: 38,233
Posted By bigmw
Why don’t you go beyond the preview step and...

Why don’t you go beyond the preview step and actually open/load the file, you will see that the full graph extends beyond the artboard area.

You can do the following things:
1 Save a png file...
Forum: Bioinformatics 03-22-2014, 05:42 AM
Replies: 92
Views: 38,233
Posted By bigmw
Someone asked a similar question here: ...

Someone asked a similar question here:
https://stat.ethz.ch/pipermail/bioconductor/2012-March/044427.html
Forum: Bioinformatics 03-21-2014, 01:18 PM
Replies: 92
Views: 38,233
Posted By bigmw
Well, you can check the first attached image in...

Well, you can check the first attached image in post 47. Obviously you do get different colors on pathview graphs. I think you might have checked the pathview output in the wrong directory:
kegg.dir...
Forum: Bioinformatics 03-21-2014, 10:13 AM
Replies: 92
Views: 38,233
Posted By bigmw
Shriram, Here is the original graph from...

Shriram,
Here is the original graph from official KEGG website:
http://www.genome.jp/kegg-bin/show_pathway?sce00051+YCL040W
With the GLK1 gene node marked by red box. Hover your mouse over there,...
Forum: Bioinformatics 03-20-2014, 06:23 PM
Replies: 92
Views: 38,233
Posted By bigmw
You donít even have pathview package loaded based...

You donít even have pathview package loaded based on your sessionInfo().
Forum: Bioinformatics 03-20-2014, 05:52 PM
Replies: 92
Views: 38,233
Posted By bigmw
May I know what node, gene, pathway and what...

May I know what node, gene, pathway and what species you are talking about?
Forum: Bioinformatics 03-19-2014, 05:07 PM
Replies: 92
Views: 38,233
Posted By bigmw
Again, that’s because in this pathway, node...

Again, that’s because in this pathway, node labelled “Gene A” includes gene(s) other than “Gene A” but with similar function. It is a summary of fold changes for all genes mapped to this node, should...
Forum: Bioinformatics 03-18-2014, 06:58 PM
Replies: 92
Views: 38,233
Posted By bigmw
If you are look for the gene entry"120"...

If you are look for the gene entry"120" underpv.out.list[[1]]$plot.data.gene, it may or may not be different from the original data, cnts.d, because multiple genes may be mapped to the same nodes in...
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