Eyoung20 journal week 8 - Revision history

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 I would like to acknowledge that the methods were taken from [[week 8]] and then adapted to fit the actual lab methods preformed.
 I would like to acknowledge [[user:kdahlquist|Dr. Dahlquist]] for her instruction on the topic and the procedure.
- "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
+"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 ==references==

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 ==references==
+LMU BioDB 2019. (2019). Week 8. Retrieved October 23, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
 {{Template:eyoung20}}

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 ==Acknowledgements==
-I would like to acknowledge my home work partners
+I would like to acknowledge my home work partners s [[User:Imacarae|Ivy]], [[User:Dmadere|Delisa]], and [[User:Msamdars|Mihir]] with there help with checking our work and helping to answer questions about the procedure.
 ==references==

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 ==Acknowledgements==
 ==references==
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 * Row 1 was selected and the menu item Data > Filter > Autofilter was selected. Little drop-down arrows appeared at the top of each column.  This enabled the data to be filtered according to criteria that was set.
 * The drop-down arrow  was clicked for the unadjusted p value. A criterion that would filter the data so that the p value had to be less than 0.05 was set.
-** '''''How many genes had p < 0.05? and what is the percentage (out of 6189)?''''':
+** '''''How many genes had p < 0.05? and what is the percentage (out of 6189)?''''': 2290/6189 37.00%
-** '''''How many genes had p < 0.01? and what is the percentage (out of 6189)?''''':
+** '''''How many genes had p < 0.01? and what is the percentage (out of 6189)?''''': 1380/6189 22.29%
-** '''''How many genes had p < 0.001? and what is the percentage (out of 6189)?''''':
+** '''''How many genes had p < 0.001? and what is the percentage (out of 6189)?''''': 691/6189 11.16%
-** '''''How many genes had p < 0.0001? and what is the percentage (out of 6189)?''''':
+** '''''How many genes had p < 0.0001? and what is the percentage (out of 6189)?''''':358/6189 5.78%
 * That action performed 6189 hypothesis tests.  The same method was then used to determine the percentages of relevant data that was present as determined by the The Bonferroni correction and The Benjamini-Hochberg correction.
-** '''''How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?'''''
+** '''''How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?''''': 151/6189 2.44%
-** '''''How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?'''''
+** '''''How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?''''':1458/6189 2.35%
 * In summary, the p value cut-off should not be thought of as some magical number at which data becomes "significant".  Instead, it is a moveable confidence level.  If there was to be confidence in the data, small p value cut-off were needed to be used. If less confidence about a gene expression change was ok and it was desired to include more genes in the analysis,  a larger p value cut-off could have been used.
 * '''''Comparing results with known data:'''''

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 == Conclusion ==
 From this weeks analysis we can conclude that 37.00% of the genes have an unadjusted  p<0.05, 22.29% p<0.01, 11.16% p<0.001, 5.78% p<0.0001.
 .44%  of the genes have a B&H p<0.05 and 2.35% a Bonferroni p<0.05.
 ==Acknowledgements==

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 [[media:BIOL367 F19 sample p-value slide ERY.pptx|dCIN5 p-value slide]]
+[[media: Stem_ERY.zip|zipped  genelist and GOlist ]]
 == Conclusion ==

← Older revision		Revision as of 06:50, 24 October 2019
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	[[media:BIOL367_F19_microarray-data_dCIN5_ERY.txt\|dCIN5_STEM txt file]]		[[media:BIOL367_F19_microarray-data_dCIN5_ERY.txt\|dCIN5_STEM txt file]]
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		+	[[media:BIOL367 F19 sample p-value slide ERY.pptx\|dCIN5 p-value slide]]
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	Your data and files section should include:		Your data and files section should include:

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 == Data and Files ==
 [[media:BIOL367_F19_microarray-data_dCIN5_ERY.xlsx|dCIN5_ANOVA spread sheet]]
 [[media:BIOL367_F19_microarray-data_dCIN5_ERY.txt|dCIN5_STEM txt file]]