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[[Daniel Jacobsen|Back to Main]] Link to useful Perl website: [http://learn.perl.org/books/beginning-perl/ Basic Perl] ==Calendar== <calendar> name=Daniel:Notebook/GenomeMiner format=%name/%year-%month-%day date=2013/02/01 view=oneyear </calendar> ==Useful Linux Commands== '''SCP to laptop''' %% scp <remote user>@<remote machine>:<remote path> <local file> scp djacobse@132.239.135.41:/home/djacobse/HL155/130628_HL155/probecount.csv probecount.csv '''Chmod of Bash Script''' chmod u+x <bashscriptname> ==HL155== Analysis of 3 probe production companies: MYcroarray, Agilent, and Custom Array. Data Analysis Spreadsheet: [[File:ProbeComparison.xlsx]] MATLAB Master File: [[File:HL155_Master.txt]] ===Raw Data=== '''Raw Data''' Methods: ([[Daniel:Notebook/GenomeMiner/2013-8-13|Dan]],[[Matt:LabNotes/2013-8-9|Matt]]) {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> |- style="font-size:12pt;font-weight:bold" | width="102" height="30" valign="bottom" | Probe Set | width="65" align="center" | Total reads | width="71" align="center" | Filtered reads | width="82" align="center" | Perfect match | width="65" align="center" | 1 ins/del | width="65" align="center" | 1 sub | width="65" align="center" | 2 ins/del | width="65" align="center" | 2 sub | width="89" align="center" | 1 ins/del & 1 sub | align="center" width="65" align="center" | 3+ |- style="font-size:12pt" |style="font-weight:bold" height="15" valign="bottom" | Mycroarray | align="center" align="center" | 20727275 | align="center" align="center" | 15082383 | align="center" align="center" | 4411040 | align="center" align="center" | 3584377 | align="center" align="center" | 2417322 | align="center" align="center" | 1893421 | align="center" align="center" | 754110 | align="center" align="center" | 1647242 | align="center" align="center" | 374871 |- style="font-size:12pt" |style="font-weight:bold" height="15" valign="bottom" | Agilent 0 gap | align="center" align="center" | 4953642 | align="center" align="center" | 4448339 | align="center" align="center" | 3294962 | align="center" align="center" | 102309 | align="center" align="center" | 808922 | align="center" align="center" | 12240 | align="center" align="center" | 129671 | align="center" align="center" | 24455 | align="center" align="center" | 75780 |- style="font-size:12pt" |style="font-weight:bold" height="15" | Agilent 20 gap | align="center" align="center" | 4052727 | align="center" align="center" | 3578431 | align="center" align="center" | 2676974 | align="center" align="center" | 101104 | align="center" align="center" | 619290 | align="center" align="center" | 14445 | align="center" align="center" | 92296 | align="center" align="center" | 20184 | align="center" align="center" | 54138 |- style="font-size:12pt" |style="font-weight:bold" height="15" | Agilent | align="center" align="center" | 9006369 | align="center" align="center" | 8026770 | align="center" align="center" | 5971936 | align="center" align="center" | 203413 | align="center" align="center" | 1428212 | align="center" align="center" | 26685 | align="center" align="center" | 221967 | align="center" align="center" | 44639 | align="center" align="center" | 129918 |- style="font-size:12pt" |style="font-weight:bold" height="15" valign="bottom" | Custom Array 12K | align="center" align="center" | 5195976 | align="center" align="center" | 4533981 | align="center" align="center" | 3176472 | align="center" align="center" | 77874 | align="center" align="center" | 962022 | align="center" align="center" | 4934 | align="center" align="center" | 178599 | align="center" align="center" | 30019 | align="center" align="center" | 104061 |} '''As Percent''' {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> |- style="font-size:12pt;font-weight:bold" | width="102" height="30" valign="bottom" | Probe Set | width="65" align="center" | Total reads | width="71" align="center" | Filtered reads (%) | width="82" align="center" | Perfect match (%Filtered) | width="65" align="center" | 1 ins/del (%Filtered) | width="65" align="center" | 1 sub (%Filtered) | width="65" align="center" | 2 ins/del (%Filtered) | width="65" align="center" | 2 sub (%Filtered) | width="89" align="center" | 1 ins/del & 1 sub (%Filtered) | width="65" align="center" | 3+ (%Filtered) |- style="font-size:12pt" |style="font-weight:bold" height="15" valign="bottom" | Mycroarray | align="center" align="center" | 20727275 | align="center" align="center" | 72.8 | align="center" align="center" | 29.2 | align="center" align="center" | 23.8 | align="center" align="center" | 16.0 | align="center" align="center" | 12.6 | align="center" align="center" | 5.0 | align="center" align="center" | 10.9 | align="center" align="center" | 2.5 |- style="font-size:12pt" |style="font-weight:bold" height="15" valign="bottom" | Agilent 0 gap | align="center" align="center" | 4953642 | align="center" align="center" | 89.8 | align="center" align="center" | 74.1 | align="center" align="center" | 2.3 | align="center" align="center" | 18.2 | align="center" align="center" | 0.3 | align="center" align="center" | 2.9 | align="center" align="center" | 0.5 | align="center" align="center" | 1.7 |- style="font-size:12pt" |style="font-weight:bold" height="15" | Agilent 20 gap | align="center" align="center" | 4052727 | align="center" align="center" | 88.3 | align="center" align="center" | 74.8 | align="center" align="center" | 2.8 | align="center" align="center" | 17.3 | align="center" align="center" | 0.4 | align="center" align="center" | 2.6 | align="center" align="center" | 0.6 | align="center" align="center" | 1.5 |- style="font-size:12pt" |style="font-weight:bold" height="15" | Agilent | align="center" align="center" | 9006369 | align="center" align="center" | 89.1 | align="center" align="center" | 74.4 | align="center" align="center" | 2.5 | align="center" align="center" | 17.8 | align="center" align="center" | 0.3 | align="center" align="center" | 2.8 | align="center" align="center" | 0.6 | align="center" align="center" | 1.6 |- style="font-size:12pt" |style="font-weight:bold" height="15" valign="bottom" | Custom Array 12K | align="center" align="center" | 5195976 | align="center" align="center" | 87.3 | align="center" align="center" | 70.1 | align="center" align="center" | 1.7 | align="center" align="center" | 21.2 | align="center" align="center" | 0.1 | align="center" align="center" | 3.9 | align="center" align="center" | 0.7 | align="center" align="center" | 2.3 |} ===Comparison=== '''Comparison of Errors''' [[Image:Probecompare_HL155.png|600px]] '''Comparing errors per 100 bp''' {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> |- style="font-size:12pt" | align="center" width="65" height="30" valign="bottom" | |style="font-weight:bold" width="108" align="center" | Insertions/Deletions (/100 bp) |style="font-weight:bold" width="91" align="center" | Substitutions (/100 bp) |- style="font-size:12pt" |style="font-weight:bold" height="30" valign="bottom" | Mycroarray | align="center" align="center" valign="bottom" | 1.20 | align="center" align="center" valign="bottom" | 0.74 |- style="font-size:12pt" |style="font-weight:bold" height="15" valign="bottom" | Agilent | align="center" align="center" valign="bottom" | 0.08 | align="center" align="center" valign="bottom" | 0.48 |- style="font-size:12pt" |style="font-weight:bold" height="30" valign="bottom" | Custom Array 12K | align="center" align="center" valign="bottom" | 0.05 | align="center" align="center" valign="bottom" | 0.60 |} '''Comparison by Error''' Y axis is given in % chance, so Agilent probes have overall error rate of ~2%, or 1 in 50 bp. [[Image:AgilentMYCA ErrorComp090313.png|600px]] ===Probe Counts Comparison=== Looking at the comparison between counts of the three companies. Bar graphs below divide the probes into 4 categories: zero, under-amplified, normally amplified, and over-amplified. All counts are normalized to the expected number of reads. Expected number of reads is calculated by dividing the total number of reads by the total number of probes in the set. The expected number of reads is therefore the number of reads if all probes were amplified equally. Under amplified probes are defined as those with less than half the number of expected reads. This is because PCR amplifies at 2^n. Having half as many reads is therefore the same as the probe being amplified one less cycle than the norm. Similarly, over-amplified is defined as having more than twice the number of reads. Again, having twice as many reads is the same as saying the probe was amplified for one extra cycle. The four categories are: '''Zero''': The probe was never counted '''Under Amplified''': probe count < 0.5*expected '''Normally Amplified''': 0.5*expected β€ probe count β€ 2*expected '''Over-amplified''': probecount > 2*expected '''Probe Count Comparison''' [[Image:Hl155_compare_rc.png|1000px]]
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