GeneChip™ HT RG-230 PM Array Plate - FAQs

View additional product information for GeneChip™ HT RG-230 PM Array Plate - FAQs (901259)

9 product FAQs found

Is the hybridization mix for cartridges the same as the hybridization mix for PEG arrays (array plates)?

The hybridization mix for PEG arrays is different from the hybridization mix for cartridges. The concentrations of the hybridization mix are different and in addition, DMSO is not added into the hybridization mix for PEG arrays because it can affect the glue that holds the PEG to the plate.

How long does it take to scan the plate?

96 arrays = 4-4.6 hours
24 arrays = 1.5-2 hours

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

If I have cartridges, can I move to PM only arrays in the middle of my project?

No, continue to finish products using the same procedures and products. New projects can be moved to PM only arrays.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

What QC metrics will I use to assess the quality of my data?

Mean absolute relative log expression: MA (RLE)
-Detection of 20X spikes, Bio B, Bio C, Bio D & Cre
-House keeping controls
-Poly A controls
-Antigenomic GC - 12 background probes
-PM mean

Please refer to the QC Metrics for Human, Mouse and Rat HT PM Array Plates QRC for more information (http://tools.thermofisher.com/content/sfs/manuals/ hmr_qc_metrics_qrc.pdf).

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Which algorithm do I use to run the analysis for these new HT PM Plate Arrays?

We recommend running the RMA algorithm in the Transcriptome Analysis Console (TAC).

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Why is MAS5 disabled?

MAS5 requires the use of Mismatch probes which the HT PM Plate Arrays do not currently use. MAS5 can be used with the Advanced Configuration however the software will automatically shut down if analysis is run.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Will I be able to use %P to assess the quality of my scans?

No, %P is a metric derived using the MAS5 algorithm which has been disabled for the HT PM Plate Arrays.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Will new scripts need to be uploaded in GCAS for the new plate?

No, new scripts for Hyb, Wash, and Stain of the HT HMR PM only array plates will not be needed. The script is the same as the old HMR plate arrays.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Is the PM only plate array content exactly the same as the cartridge?

No, the PM only arrays have probes that are perfect match only. The mismatch probes have been removed. For the HT HGU133 plus PM product roughly 3/4 of the probesets have 9 probes, a small portion has 10; the remaining probesets have 11. The Mouse and Rat PM only plate arrays utilize all 11 probes for each probeset.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.