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Forum: Bioinformatics 03-05-2011, 04:04 PM
Replies: 21
Views: 14,777
Posted By Sol
Please I did the transcriptome SOLID, but...

Please


I did the transcriptome SOLID, but reads not fully aligned, I'm losing 16 million of the data. what happened? where can I find? which software to use? I used the Bioscope. Can I use phred...
Forum: RNA Sequencing 11-22-2010, 05:43 PM
Replies: 155
Views: 69,501
Posted By Sol
How do you do to calculated the cutoff in the...

How do you do to calculated the cutoff in the value the DEGseq, in pvalue. cutoff = 2 for example
thanks
Forum: Bioinformatics 11-22-2010, 05:40 PM
Replies: 1
Views: 1,912
Posted By Sol
How do you do to calculated the cutoff the...

How do you do to calculated the cutoff the diferenttial gene expression??
thanks
Forum: RNA Sequencing 11-20-2010, 05:26 PM
Replies: 155
Views: 69,501
Posted By Sol
I would like know what the letters NA means as a...

I would like know what the letters NA means as a result of DEGSeq.
Another question: log2 is two fold change or four fold change
thanks
Forum: RNA Sequencing 11-15-2010, 09:18 AM
Replies: 10
Views: 18,473
Posted By Sol
Question RPKM-normalization

Please, how do to normalize the data from SOLiD? I'll do differential expression. RPKM is the standardization? What does that mean exactly
thanks
Forum: RNA Sequencing 11-15-2010, 06:31 AM
Replies: 10
Views: 24,858
Posted By Sol
Good morning.I need to normalize the data leaving...

Good morning.I need to normalize the data leaving the software analysis of SOLiD, Bioscope?
I need to normalize?
thanks
Forum: RNA Sequencing 10-27-2010, 01:20 PM
Replies: 155
Views: 69,501
Posted By Sol
the results of the DEGseq, already can be used...

the results of the DEGseq, already can be used directly for analysis or should i make some other standardization
thanks
Forum: RNA Sequencing 10-27-2010, 01:00 PM
Replies: 10
Views: 24,858
Posted By Sol
I need to take in the graph generated in MA-plot...

I need to take in the graph generated in MA-plot DEGseq, the differentially expressed genes. has some software that does this? or script?
thanks
Forum: RNA Sequencing 10-27-2010, 12:09 PM
Replies: 155
Views: 69,501
Posted By Sol
What is the function of the MA plot the fold...

What is the function of the MA plot the fold change??
The graph shows the relationship in the MA-plot, no??
thanks
Forum: RNA Sequencing 10-27-2010, 10:31 AM
Replies: 155
Views: 69,501
Posted By Sol
but, what is the mean RPKM? thanks

but, what is the mean RPKM?
thanks
Forum: RNA Sequencing 10-27-2010, 10:01 AM
Replies: 155
Views: 69,501
Posted By Sol
Thanks and the RPKM. how to normalize the...

Thanks

and the RPKM. how to normalize the data?
I divide the number of reads by the size of the gene and divide by all the reads?
How it is calculated
thanks
Forum: RNA Sequencing 10-27-2010, 09:14 AM
Replies: 155
Views: 69,501
Posted By Sol
but, o z-score, is based on what data? and what...

but, o z-score, is based on what data? and what is difference between q-value and p-value. I don't understand.
Thanks
Forum: RNA Sequencing 10-26-2010, 11:54 AM
Replies: 155
Views: 69,501
Posted By Sol
Hi I ran the program DEGexp of the DEGseq. The...

Hi
I ran the program DEGexp of the DEGseq. The output file generated a table with values of log2 fold change, z-score, p-value, q-value and signature (p-value <0.001). How to interpret the gene...
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