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Using MapMan

Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray annotations

Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray annotations
agilent sureprint g3 differential gene expression human
Answer
11/17/16 4:47 AM
I have used Agilent SurePrint G3 Human Gene Expression v3 for my analysis. Trying to analyze the data using Robina I have encountered a few problems:

1) I can not find the probe annotation for this chip in the mapman? Does that exist?

2) If each of my groups contain only one sample, using limma as strategy the software doesn't start the analysis and if I use RankProduct as strategy, the program returns the error:

Error in RPadvanceV1(data, cl, origin, num.perm, logged, na.rm, gene.names, :
Number of classes and/or origins should match the columns in the data
Calls: RPadvance -> RPadvanceV1
Execution halted

3) If I do not have replicates for control and treatment, Is there any way to find Deferentially expressed genes using Robina?

4) I have 16GB RAM computer but Robina keeps freezing, warning RAM insufficinecy error while its not even using 25% of total free RAM. It says in FAQ part of manual it has been explained how to solve this issue in detail. But There is no such section in manutal included in the software.

5) In the tutorial included in the software, it is mentione that for MA plot robina calculates the >LFC1 values and also Relative logarithmic expression (RLE) and NUSE graph and RNA degradation graph. But in the latest version of Robina that is v 1.2.4, these values and graphs are not produced in QC section.

Thank you in advance