GeneChip™ HT HG-U133+PM Array Plate - FAQs

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11 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.

What does the "_x_at" extension represent in the HG-U133 probe set name?

Occasionally, it is not possible to select either a unique probe set or a probe set with all probes common among multiple transcripts ("_s_at" ). In such cases, similarity criteria are suspended, and the resulting probe set name is appended with the "_x_at" extension. These probe sets contain some probes that are identical, or highly similar, to unrelated sequences. These probes may cross-hybridize in an unpredictable manner with sequences other than the main target. Data generated from these probe sets should be interpreted with caution, due to the likelihood that some of the signal is from transcripts other than the one being intentionally measured.

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

What does the "_s_at" extension represent in the HG-U133 probe set name?

The primary goal in probe set selection is to select a probe set unique to a single transcript or common among a small set of similar transcript variants. A probe set name is appended with the "_s_at" extension when all the probes exactly match multiple transcripts. The probe set selection process generally favors probe sets measuring fewer transcripts. Probe sets with common probes among multiple transcripts (the "_s_at" probe sets), are frequent and are to be expected, due to alternative polyadenylation and alternative splicing. In most cases, "_s_at" probe sets represent transcripts from the same gene, but the same probe set can sometimes also represent transcripts from homologous genes. One transcript may be represented by both a unique and an "_s_at" probe set when the transcript variation is sufficient.

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

How long does it take to scan the plate?

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

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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.

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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.

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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.

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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.