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		CGH file upload for data conversion and analysis
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</div>
	<div  id="iconLegend" style="display: none;">
<div class="section ">
		<div style="float: left; width: 27px; height: 30px; margin: 3px;">
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			subset specific data and / or visualizations
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			<img src="/p/icnArrayMap.png" />
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			arrayMap - genomic array data in cancer 
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			<img src="/p/icnPubs.png" />
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			publication data
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			<img src="/p/icnArrays.png" />
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		<div class="tiny" style="float: left; width: 160px; height: 30px; margin: 3px; text-align: left;">
			array specific data
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			<img src="/p/icnGEO.png" />
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			data at NCBI GEO
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			<img src="/p/icnSeries.png" />
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			genomic copy number data in cancer: experimental series
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			<img src="/p/icnICDM.png" />
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			genomic copy number data in cancer: ICD-O 3 morphologies
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			additional information / help
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			genomic copy number data in cancer: clinical or diagnostic groups
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			array probe level plots
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			array platform data
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			aCGH publication data
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			sample details
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			Progenetix - genomic copy number aberrations in cancer
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			data at ArrayExpress / EMBL-EBI
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			<img src="/p/icnICDT.png" />
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			genomic copy number data in cancer: tumor topographies / locations
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			<img src="/p/icnPubsCCGH.png" />
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			cCGH publication data
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			<img src="/p/icnPubMed.png" />
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			article in PubMed
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</div>
</div>
<div class="section ">
	<form
		
		action="/cgi-bin/pgFileLoader.cgi"
		method="post"
		target="_self"
		enctype="multipart/form-data"
	>
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		Load file
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	<div class="labelbox " style="">
		File format
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	<div class="centerbox " style="  ">
		
		<select  name="uploadFileFormat" class="formfield">
			<option value="ProgenetiXMLJSONpost" >ProgenetiXML or JSON, pre-analyzed</option>
			<option value="ISCN" >ISCN annotation table: sampleID | ish CGH</option>
			<option value="progenetixsegments" >segments list: sampleID | chromosome | base_start | base_end | status</option>
			<option value="namedprojectsegments" >segments list: project ID | sampleID | chromosome | base_start | base_end | status</option>
			<option value="affymetrixsegments" >segments list: sampleID | chromosome | base_start | base_end | mean | probes</option>
			<option value="agilentsegments" >segments list: sampleID | chromosome | base_start | base_end | probes | inf_probes | mean</option>
			<option value="harvardsegments" >segments list: sampleID | chromosome | base_start | base_end | probes | mean</option>
		</select>
	</div>
	<div class="helpbox">
		<a class="help" href="">[?]
			<span>Please select the apppropriate format of your upload file.</span>
		</a>
	</div>
	<div class="labelbox " style="">
		Technique
	</div>
	<div class="centerbox " style="  ">
		
		<select  name="technique" class="formfield">
			<option value="aCGH" >array CGH (incl. single color)</option>
			<option value="cCGH" >chromosomal CGH</option>
		</select>
	</div>
	<div class="helpbox">
		<a class="help" href="">[?]
			<span>Please select the apppropriate format of your upload file.</span>
		</a>
	</div>
	<div class="labelbox " style="">
		LOSS/GAIN THRESHOLDS
	</div>
	<div class="centerbox " style="  ">
		
		<div class="formfield">
			<div style="width: 48%; float: left; text-align: center;">
				<input type="text" name="segLossThresh" maxlength="6" value="-0.15" style="width: 40%; float: left;" />
				-
				<input type="text" name="segGainThresh" maxlength="6" value="0.15" style="width: 40%; float: right;" />
			</div>
			<div style="width: 48%; float: right; ">

			</div>
		</div>
	</div>
	<div class="helpbox">
		<a class="help" href="">[?]
			<span>Cut-offs from which a segment is considered a genomic loss or gain. The Y axis factor allows the modification of the Y scaling.</span>
		</a>
	</div>
	<div class="labelbox " style="">
		REGION SIZE
	</div>
	<div class="centerbox " style="  ">
		
			<div class="formfield">
				<div style="width: 48%; float: left; text-align: center;">
					<input type="text" name="minSegSize" maxlength="9" placeholder="0 kb" value="" style="width: 40%; float: left;" />
					-
					<input type="text" name="maxSegSize" maxlength="9" placeholder="250000 kb" value="" style="width: 40%; float: right;" />
				</div>
				<div style="width: 48%; float: right; ">
					<div class="labelbox" style="width: 45%; float: left; font-size: 0.9em;">
					Min. Probes
					</div>
					<input type="text" name="minSegCount" maxlength="6" value="2" style="width: 40%; float: right;" />
				</div>
			</div>
	</div>
	<div class="helpbox">
		<a class="help" href="">[?]
			<span>Limit displayed regions to a specific size range (in kB). Smaller CNVs will be removed.</span>
		</a>
	</div>
	<div class="labelbox">
	&#160;
	</div>
	<div class="centerbox">
		<input type="submit" name="submit" value="Load file" class="formfield"/>
	</div>
	</form>
</div>
	<div class="section tiny">
		These tools were  developed for our research projects. You are welcome to
		try them out, but there is only <a href="/pgwiki/pmwiki.php">sparse documentation</a>. If more support and/or custom analysis
		is needed, please contact <a href="http://www.imls.uzh.ch/baudis/" target="_blank">Michael Baudis</a>
		regarding a collaborative project.
	</div>
	<div id="footer" class="section">
		&#169; 2000 - 2012 <a href="http://www.imls.uzh.ch/research/baudis/">Michael Baudis</a>,
		refreshed Sun, 20 May 2012 00:27:11 GMT. No responsibility is taken for the correctness<br />
		of the data presented nor the  results achieved with the Progenetix tools.
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