RNA-Seq analysis using MeV

[hlwright]

I have an Excel file (tab delimited .txt) of count data generated using htseq which I am trying to upload into MeV for RNA-Seq analysis using

File - Load Data - Select File Loader - RNASeq DGE/RPKM Files

MeV is 'hanging' with the "Slide Data Loading" popup showing 0% progress. I have seen on the MeV SourceForge forum that upload problems can be solved by formatting all data as "text" in Excel before saving as .txt file. This has not worked for me. Please can anyone help? I posted this query on the MeV SourceForge help forum two weeks ago but have had no reponse (I'm not sure how well used it is). There is also no email address that I can find for MeV assistance.

For info, I am using Mac OS X 10.6.8, MeV is v4.8.1, Java is v1.6.0, Java 3D is v1.3.1 (I have also tried this on a Windows XP machine and get the same error).

Thanks in advance
Helen

[sisch]

Would you mind posting the first few lines of your "text" file in a code tag here? That would make troubleshooting much easier.

Simon

[hlwright]

Hi Simon

Thanks for replying so quickly. Having struggled over this for 2 weeks I think I have now managed to work it out by myself (the power of posting on SeqAnswers!). I didn't have all the "required" fields in columns A-E. My data now looks like this and will load:

tracking_id	locus	nearest_ref_id	class_code	transcript_length	Sample1	Sample2	Sample3	Sample4	Sample5	Sample6 
1/2-SBSRNA4	chr4:110351118-110354973	-			15	10	6	12	10	18
A1BG	chr19:58858171-58864865	-			12	17	20	15	12	6
A1BG-AS1	chr19:58863335-58866549	-			9	15	7	9	2	2
A1CF	chr10:52559168-52645435	-			2	0	1	1	0	0
A2LD1	chr13:101182417-101241046	-			16	16	16	20	4	6

However, when I start to do either edgeR or DESeq analysis MeV just vanishes (I presume its crashing). I have increased the java memory to 2GB and have tried running on just a small dataset of 4 samples vs 4 samples. My dataset is quite large (>20 samples).

Any ideas?

Thanks
Helen

[hlwright]

Postscript to my last message, I think the crashing may be a Mac OS problem, as I have managed to run edgeR on a small dataset on a Windows machine, plus MeV crashes on the Mac using the supplied sample dataset.

I realise I have pretty much answers my own questions here, but hopefully this post might help someone else in the future!

Helen