Tutorial Data - Revision history

Smith: /* Tutorial data files */

2015-03-11T20:19:39Z

‎Tutorial data files

Smith: /* Tutorial data files */

2015-03-11T20:18:49Z

‎Tutorial data files

Smith: /* Tutorial data files */

2015-03-11T19:08:52Z

‎Tutorial data files

Smith: /* Tutorial data files */

2015-03-11T19:08:23Z

‎Tutorial data files

Smith: /* Generation of the "webmatrix2_quantile_log2_dev1.2_mv0.exp" dataset. */

2011-11-14T21:28:46Z

‎Generation of the "webmatrix2_quantile_log2_dev1.2_mv0.exp" dataset.

Smith: moved Tutorial - Data to Tutorial Data

2010-12-09T22:16:22Z

moved Tutorial - Data to Tutorial Data

Smith: /* More about Bcell-100.exp */

2009-07-23T21:50:28Z

‎More about Bcell-100.exp

Smith: /* More about Bcell-100.exp */

2009-07-23T21:22:50Z

‎More about Bcell-100.exp

Smith: /* Tutorial data files */

2009-07-23T21:12:21Z

‎Tutorial data files

Smith: /* Generation of the "webmatrix2_quantile_log2_dev1.2_mv0.exp" dataset. */

2009-07-23T21:00:04Z

‎Generation of the "webmatrix2_quantile_log2_dev1.2_mv0.exp" dataset.

← Older revision		Revision as of 20:19, 11 March 2015
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−	[[Media~~:File~~:Bcell-100_log2.zip\|Bcell-100_log2.zip]] is the BCell-100 data normalized with the Threshold Normalizer, with the minimum value set to 1.0, and then log2 transformed.	+	[[Media:Bcell-100_log2.zip\|Bcell-100_log2.zip]] is the BCell-100 data normalized with the Threshold Normalizer, with the minimum value set to 1.0, and then log2 transformed.

← Older revision		Revision as of 20:18, 11 March 2015
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	==Tutorial data files==		==Tutorial data files==
	The file [[Media:Bcell-100.zip\|Bcell-100.zip]] contains the file Bcell-100.exp, which is a geWorkbench data matrix format file containing 100 Bcell experiments using Affymetrix U95-Av2 chips. It contains the same data as the file "webmatrix2.exp" which has been used in the tutorials previously. The array groups have been given more descriptive names. The data has been processed using the Affymetrix MAS5 normalization routine. It comes from the lab of Dr. Ricardo Dalla-Favera at the Institute for Cancer Research at Columbia University. The 100 arrays represent B-cell experiments drawn from a variety of conditions, including cancerous and normal, germinal center and non-germinal center.		The file [[Media:Bcell-100.zip\|Bcell-100.zip]] contains the file Bcell-100.exp, which is a geWorkbench data matrix format file containing 100 Bcell experiments using Affymetrix U95-Av2 chips. It contains the same data as the file "webmatrix2.exp" which has been used in the tutorials previously. The array groups have been given more descriptive names. The data has been processed using the Affymetrix MAS5 normalization routine. It comes from the lab of Dr. Ricardo Dalla-Favera at the Institute for Cancer Research at Columbia University. The 100 arrays represent B-cell experiments drawn from a variety of conditions, including cancerous and normal, germinal center and non-germinal center.
		+
		+
		+	[[Media:File:Bcell-100_log2.zip\|Bcell-100_log2.zip]] is the BCell-100 data normalized with the Threshold Normalizer, with the minimum value set to 1.0, and then log2 transformed.

← Older revision		Revision as of 19:08, 11 March 2015
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−	The file [[Media:Tutorial_data.zip]] (3.586 MB) contains data files in several different formats useful for the tutorials or just trying out geWorkbench. It contains the following files:	+	The file [[Media:Tutorial_data.zip\|Tutorial_data.zip]] (3.586 MB) contains data files in several different formats useful for the tutorials or just trying out geWorkbench. It contains the following files:

	*'''cardiogenomics.med.harvard.edu/''' -Contains 10 individual MAS5/GCOS format data files.		*'''cardiogenomics.med.harvard.edu/''' -Contains 10 individual MAS5/GCOS format data files.

@@ Line 5: / Line 5: @@
 ==Tutorial data files==
 The file [[Media:Bcell-100.zip|Bcell-100.zip]] contains the file Bcell-100.exp, which is a geWorkbench data matrix format file containing 100 Bcell experiments using Affymetrix  U95-Av2 chips.  It contains the same data as the file "webmatrix2.exp" which has been used in the tutorials previously.  The array groups have been given more descriptive names. The data has been processed using the Affymetrix MAS5 normalization routine.  It comes from the lab of Dr. Ricardo Dalla-Favera at the Institute for Cancer Research at Columbia University.  The 100 arrays represent B-cell experiments drawn from a variety of conditions, including cancerous and normal, germinal center and non-germinal center.
-The file "tutorial_data.zip" contains the following files:
+The file [[Media:Tutorial_data.zip]] (3.586 MB) contains data files in several different formats useful for the tutorials or just trying out geWorkbench.  It contains the following files:
 *'''cardiogenomics.med.harvard.edu/''' -Contains 10 individual MAS5/GCOS format data files.

← Older revision		Revision as of 21:28, 14 November 2011
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	http://cardiogenomics.med.harvard.edu/groups/proj2/pages/Hs-belgium_home.html		http://cardiogenomics.med.harvard.edu/groups/proj2/pages/Hs-belgium_home.html
−
−
−
−	~~==Generation of the "webmatrix2_quantile_log2_dev1.2_mv0.exp" dataset.==~~
−	webmatrix2_quantile_log2_dev1.2_mv0.exp is derived from the same original dataset as Bcell-100.exp described above. For use in the tutorials we normalized and filtered the data. The steps shown below are just an example of how filtering and normalization can be used, and each dataset should be handled according to the type of analysis being undertaken and its goals.
−
−	~~The dataset was created by the following steps:~~
−	~~# Normalization: Quantile normalization.~~
−	~~# Normalization: Log2 transformation.~~
−	~~# Filtering: Deviation filter with Deviation bound of 1.2.~~
−	~~# Filtering: Missing values filter with maximum number of missing arrays of 0.~~
−	# Finally, for convenience, the first marker, which is used to identify the type chip being used, was added back (it is filtered out above). This merely removes the needed to identify the chip type manually on loading.
−
−	~~The result of performing these steps is available as the file "webmatrix2_quantile_log2_dev1.2_mv0.exp", found in the tutorial data [[Download]] file "tutorial_data.zip".~~

← Older revision	Revision as of 22:16, 9 December 2010
(No difference)

@@ Line 32: / Line 32: @@
 # CLL/P-CLL - B cell chronic lymphocytic leukemia (P indicates purified, otherwise not)
 # BL - Burkitt lymphoma
-# DLCL - diffuse large B cell lymphoma (DLBCL)
+# DLCD/DLCL - purified DLBCL
 # FL - follicular lymphoma
 # HCL - hairy cell leukemia
 # PEL - primary effusion lymphoma
-# D - ?
+# D - DLBCL
 Non-cancerous
-# CB - cord blood
+# CB - centroblasts
-# CC - ?
+# CC - centrocytes
-# M - memory
+# M - memory B cells
-# N - naive
+# N - naive B cells
 ==About the cardiogenomics microarray dataset==

@@ Line 25: / Line 25: @@
 * '''ClusterTree38_Sequences.fasta''' -Contains sequences derived from hierarchical clustering (old example).
 * '''cluster_tree_12markers.csv''' -Contains a list of markers derived from hierarchical clustering (old example).
 ==About the cardiogenomics microarray dataset==

@@ Line 45: / Line 45: @@
 ==Generation of the "webmatrix2_quantile_log2_dev1.2_mv0.exp" dataset.==
+webmatrix2_quantile_log2_dev1.2_mv0.exp is derived from the same original dataset as Bcell-100.exp described above. For use in the tutorials we normalized and filtered the data.  The steps shown below are just an example of how filtering and normalization can be used, and each dataset should be handled according to the type of analysis being undertaken and its goals.
 The dataset was created by the following steps: