Kzebrows Week 12 - Revision history

Kzebrows: /* Electronic Lab Notebook */ edit verification w/Coder and QA

2015-12-07T00:20:01Z

‎Electronic Lab Notebook: edit verification w/Coder and QA

Kzebrows: fix link

2015-11-24T05:58:39Z

fix link

Kzebrows: minor deletion

2015-11-24T05:57:26Z

minor deletion

Kzebrows: /* Electronic Lab Notebook */ minor edit

2015-11-23T01:15:12Z

‎Electronic Lab Notebook: minor edit

Kzebrows: minor edits to lab notebook

2015-11-23T01:14:36Z

minor edits to lab notebook

@@ Line 14: / Line 14: @@
 We then combined all files into one master data file by copying/pasting the spreadsheets into one document and uploaded it to the team's file page found [[OTS Files | here]].
-In order to verify that the gene IDs in the data match the chosen species and strain being used to create the .gdb, we consulted with the QA person and Coder.
+In order to verify that the gene IDs in the data match the chosen species and strain being used to create the .gdb, we consulted with the QA person and Coder. We verified that the gene IDs were in fact in the format of SF####, which was consistent with the strain being used to create the .gdb.
 ==Class Notes 11/19==

@@ Line 10: / Line 10: @@
 *RX-0.5-10-rep2
 *LR RX-0.5-10-rep2
-and so on. I did all of the RX samples (18 total files) and Erich did all of the RP samples (18 total files). We created a table found [[OTS Files | here][ showing the correspondence of the samples with the files. There were 36 files but each file corresponds to a hybridized control/treatment sample; e.g. GSM815858.gpr corresponds to GSM815858 1 (treatment) and GSM815858 2 (control).
+and so on. I did all of the RX samples (18 total files) and Erich did all of the RP samples (18 total files). We created a table found [[OTS Files | here]] showing the correspondence of the samples with the files. There were 36 files but each file corresponds to a hybridized control/treatment sample; e.g. GSM815858.gpr corresponds to GSM815858 1 (treatment) and GSM815858 2 (control).
 We then combined all files into one master data file by copying/pasting the spreadsheets into one document and uploaded it to the team's file page found [[OTS Files | here]].

@@ Line 14: / Line 14: @@
 We then combined all files into one master data file by copying/pasting the spreadsheets into one document and uploaded it to the team's file page found [[OTS Files | here]].
-In order to verify that the gene IDs in the data match the chosen species and strain being used to create the .gdb, we consulted with the QA person and Coder. We determined that
+In order to verify that the gene IDs in the data match the chosen species and strain being used to create the .gdb, we consulted with the QA person and Coder.
 ==Class Notes 11/19==

@@ Line 3: / Line 3: @@
 First, I accessed the microarray data from [[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/files/ ArrayExpress]] and downloaded the files labeled "E-GEOD-32978.sdrf.txt" and "E-GEOD-32978.raw.1.zip."
-We then analyzed the data by opening the sdrf.txt file. From examining this file it was apparent that no dye swaps had occurred. We looked at the Comment [Sample_Title] column compared to the Label and FactorValue[TREATMENT] columns and found that each sample/control combo was repeated three times leading to a total of 72 samples, but each control was labeled with Cy3 dye and each treated sample was labeled with Cy5 dye. This was the extent of samples that occurred, which is improper technique, because the dyes have different affinities. This could potentially skew the results but we moved forward with our analysis.
+We then analyzed the data by opening the sdrf.txt file. From examining this file it was apparent that no dye swaps had occurred. We looked at the Comment [Sample_Title] column compared to the Label and FactorValue[TREATMENT] columns and found that each sample/control combo was repeated three times leading to a total of 72 samples, but each control was labeled with Cy3 dye and each treated sample was labeled with Cy5 dye. This was the extent of samples that occurred which is improper technique because the dyes have different affinities. This could potentially skew the results but we moved forward with our analysis.
 Next, I unzipped the raw data file, which expanded to 36 files. Each file contains a treatment and a control hybridized. We eliminated extraneous columns, leaving behind only Column E ("ID") and Column AS ("Log Ratio 635/535"). Because each file has columns with these titles, Column E was re-labeled based on the sample and repetition. Column AS had the same label except it began with LR indicating that it was the hybridized log ratio column. Columns therefore looked like this:

@@ Line 1: / Line 1: @@
 ==Electronic Lab Notebook==
-First, I accessed the microarray data from [[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/files/ ArrayExpress]] and downloaded the files labeled "E-GEOD-32978.sdrf.txt" and "E-GEOD-32978.raw.1.zip"
+First, I accessed the microarray data from [[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/files/ ArrayExpress]] and downloaded the files labeled "E-GEOD-32978.sdrf.txt" and "E-GEOD-32978.raw.1.zip."
-First we analyzed the data by opening the sdrf.txt file. From examining this file it was apparent that no dye swaps had occurred. We looked at the Comment [Sample_Title] column compared to the Label and FactorValue[TREATMENT] columns and found that each sample/control combo was repeated three times leading to a total of 72 samples, but each control was labeled with Cy3 dye and each treated sample was labeled with Cy5 dye. This was the extent of samples that occurred, which is improper technique, because the dyes have different affinities. This could potentially skew the results but we moved forward with our analysis.
+We then analyzed the data by opening the sdrf.txt file. From examining this file it was apparent that no dye swaps had occurred. We looked at the Comment [Sample_Title] column compared to the Label and FactorValue[TREATMENT] columns and found that each sample/control combo was repeated three times leading to a total of 72 samples, but each control was labeled with Cy3 dye and each treated sample was labeled with Cy5 dye. This was the extent of samples that occurred, which is improper technique, because the dyes have different affinities. This could potentially skew the results but we moved forward with our analysis.
 Next, I unzipped the raw data file, which expanded to 36 files. Each file contains a treatment and a control hybridized. We eliminated extraneous columns, leaving behind only Column E ("ID") and Column AS ("Log Ratio 635/535"). Because each file has columns with these titles, Column E was re-labeled based on the sample and repetition. Column AS had the same label except it began with LR indicating that it was the hybridized log ratio column. Columns therefore looked like this:
@@ Line 10: / Line 10: @@
 *RX-0.5-10-rep2
 *LR RX-0.5-10-rep2
-and so on. I did all of the RX samples (18 total files) and Erich did all of the RP samples (18 total files). We created a table found [[OTS Files | here][ showing the correspondence of the samples with the files. There were 36 files but each file corresponds to a hybridized control/treatment sample; e.g. GSM815858.gpr corresponds to GSM815858 1 and GSM815858 2.
+and so on. I did all of the RX samples (18 total files) and Erich did all of the RP samples (18 total files). We created a table found [[OTS Files | here][ showing the correspondence of the samples with the files. There were 36 files but each file corresponds to a hybridized control/treatment sample; e.g. GSM815858.gpr corresponds to GSM815858 1 (treatment) and GSM815858 2 (control).
 We then combined all files into one master data file by copying/pasting the spreadsheets into one document and uploaded it to the team's file page found [[OTS Files | here]].