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Search: Posts Made By: sindrle
Forum: Bioinformatics 03-30-2014, 12:16 PM
Replies: 92
Views: 38,191
Posted By sindrle
I have not done a direct comparison yet, but I...

I have not done a direct comparison yet, but I will in the future.
Forum: Bioinformatics 03-29-2014, 04:38 AM
Replies: 92
Views: 38,191
Posted By sindrle
I have done a quick test with GOseq, but I must...

I have done a quick test with GOseq, but I must admit I like GAGE better after first glance. Easy to follow, nice manual, nice plots, lots of results and possibilities. It really facilitates further...
Forum: Bioinformatics 03-24-2014, 01:33 PM
Replies: 92
Views: 38,191
Posted By sindrle
Thank you! Another question, why is it...

Thank you!


Another question, why is it that the absolute expression levels of genes is not important when doing GAGE/GOseq/DAVID etc.?

If you have a new cell type/tissue or even a species,...
Forum: Bioinformatics 03-22-2014, 05:46 AM
Replies: 92
Views: 38,191
Posted By sindrle
Hm. Ok, Ill try Adobe Illustrator, I tried...

Hm.
Ok, Ill try Adobe Illustrator, I tried Preview, but there they were capped as well...

I ended up editing it in Excel, cropping of the names and copy them in again from the...
Forum: Bioinformatics 03-21-2014, 07:20 AM
Replies: 92
Views: 38,191
Posted By sindrle
Another question... How to alter the heatmaps...

Another question... How to alter the heatmaps text-part size (KEGG pathway names)?
The names are all capped, its unreadable.. The "pdf.size" - option only regualtes the graphic part.
...
Forum: Bioinformatics 03-21-2014, 02:50 AM
Replies: 92
Views: 38,191
Posted By sindrle
Pasted wrong sessioninfo.. # > sessionInfo()...

Pasted wrong sessioninfo..

# > sessionInfo()
# R version 3.0.3 (2014-03-06)
# Platform: x86_64-apple-darwin10.8.0 (64-bit)

# locale:
# [1]...
Forum: Bioinformatics 03-20-2014, 04:59 AM
Replies: 92
Views: 38,191
Posted By sindrle
Im having problems with Pathview. I can only get...

Im having problems with Pathview. I can only get native KEGG, the kegg.native=F does not work.

Also the native KEGG only has green color, not red (up regulated) and green (down regulated).

Why...
Forum: Bioinformatics 03-18-2014, 11:06 AM
Replies: 92
Views: 38,191
Posted By sindrle
Ok, thanks! I was thinking about the same, but...

Ok, thanks!
I was thinking about the same, but I figured since I have already ran HTseq I just used the results from there.

Good to know until next time.
Forum: Bioinformatics 03-18-2014, 04:14 AM
Replies: 92
Views: 38,191
Posted By sindrle
Im a retard. Forgot to convert kegg.gs to gene...

Im a retard. Forgot to convert kegg.gs to gene symbols:

data(egSymb)

kegg.gs.sym<-lapply(kegg.gs, eg2sym)
Forum: Bioinformatics 03-17-2014, 03:04 PM
Replies: 92
Views: 38,191
Posted By sindrle
Couldnt get gnCnt to work, I read in HTseq files...

Couldnt get gnCnt to work, I read in HTseq files instead like this:

fls <- list.files(path="~/RNAseq/02_MG-myocytes/MG_Myocytes_HTSeq/A1A2pT2D",pattern="*.txt", full.names =T)

#tab separated...
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