dChip: View array image

Export image Export CEL file Handle image contamination

Click the “CEL Image” icon in the left pane to expand the blue image icons for arrays. Click an array name on the left pane to display its image (this step may be performed before “Analysis/Normalize”):

Since the displaying dynamic range is from the 1%-qauntile (below this intensity the color is black) to the 95%-qauntile (beyond this intensity the color is the brightest yellow) of all PM and MM probe intensities in the array, images for different arrays have similar overall brightness visually, regardless of the actual brightness of a scanned image.

Click inside the array image to activate the “Image View”. The blinking blue bar (or the scattered blinking CELs) indicates the “current” probe set. Click other image areas or use the “Home” and “End” keys to highlight other probe sets. In the bottom status bar some information is displayed: the array name, the current probe set name (with number of probe pairs and the presence call), the intensity value at the current cursor position, and whether the current CEL data is normalized or not. Press “Enter” or select the menu “View/PM/MM Data” to view the data for the current probe set.

Use the arrow keys to zoom in and out the array image: “Right” or “Down” keys for larger image and “Left” or “Up” keys for smaller image. Here is an enlarged image of the PM and MM features of a probe set:

The newer chips have the “distributed probe set format”, where the probe pairs of the same probe set are scattered into the various places on the chip. This is to prevent a local image contamination to completely destroy the PM and MM information of a probe set. Toggle the menu “Image/Probe Together” (“Image/Unscrambled” in V1.2-) to reorganize the chip layout so the probe pairs for the same probe set appear adjacent in the array image.

Export image

In the dChip graphic views such as “CEL Image view” and “PM/MM data view”, the images can be saved by the “View/Export Image” menu. The BMP format has better quality, and the JPG format has smaller file size. In addition, EMF (Windows Enhanced Metafile) format is a vector format and can be enlarged without losing resolution, thus suitable for publication quality. These exported image files can be viewed by Microsoft Paint (BMP format) or Internet Explorer (JPG format), or inserted in Word or PowerPoint files by “Insert/Picture/From file” (all formats).

To convert dChip exported EMF files into EPS format, one may try the following by using Adobe Acrobat and Adobe Illustrator: (1) “Insert/Picture/From file” the EMF file into Word; (2) In Word, use “File/Print” and select Printer Name as “Acrobat PDFWriter” to crate a PDF file; (3) Use Adobe Illustrator to open the PDF file, may do some editing, and then save into AI or EPS format. Alternatively in step (2) one may use the Word “Print” and check “Print to file” (rename the file extension to .PS) to write a PS file, but this file may be in black and white and cannot be edited in Adobe Illustrator.

In V1.3+, one may also check the “Copy to clipboard” option in “View/Export image” to copy the image to the clipboard in BMP or EMF format.

Export CEL file

After Image contamination correction or normalization, one may use “Image/Export CEL” to export probe level data of one or all arrays into CEL files. If model-based expressions have been calculated, the single outliers and array outliers will be recorded in the [OUTLIERS] section of the CEL file. One can check the option “Export probe set name, probe pair order and PM/MM indication” to export additional data columns correlating a probe cell to its corresponding probe sets.

The dChip-generated CEL file does not have the standard deviation and number of pixel information in the original CEL file. As a result Affymetrix MAS5 software cannot recognize dChip-generated CEL files.

Image contamination correction

Some images may have obvious local contaminations (left picture). If not handled properly such contamination can affect downstream normalization and expression level comparison. Assuming the contamination is “additive” on the true signals and bahave like a semi-transparent layer (more discussion in Schadt et al. 2000), we implemented the image gradient correction algorithm in dChip. In “CEL Image” view (check “Use unnormalized data” when “Open Group”, uncheck “Image/Unscrambled”), one can use right-click (left-click to cancel, double-right-click to end) to outline a contaminated image region (left picture):

then select “Image/Gradient Correction” to adjust the background brightness of this region to a similar level as the background of the surrounding region. The background of a CEL is defined as the median of the CEL values in the 7*7 square centering around this CEL, and is calculated for CELs in the outlined region as well as the surrounding region extending out by 7 CELs (middle picture). Then a CEL value in the outlined contaminated region is adjusted by the difference between its background and the median background of the extended surrounding region (right picture).

When the contamination totally disguises the real signals (left picture):

we may use “Image/Replace Value” to replace each CEL value in the outlined region by the median value of this CEL in all other arrays (right picture).

Select “Undo Last” to reverse the last “Gradient Correction” or “Replace Value” operation, and “Save DCP file” to store the corrected image back into DCP files. Re-normalizing arrays (check “ignore the normalized data” in the “Analysis/Normalize” dialog) is needed, especially after the baseline array is corrected.