Editing
Matt:LabNotes/2015-4-8
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
===Regression Analysis=== *DARTFISH Data: **Px-px decoding of PGP1f V4 (S2 & S5) **Px-px decoding of PGP1f V7 (S1) **Px-px decoding of BA8 V4 (S1) **V4 and V7 in vitro counts *PGP1f RNA-seq Data *PGP1f BeadArray Data *PGP1f FISSEQ Data *[[Media:RCommands_CA12kNov2014_V7CaptureAnalysis.txt | R Commands]] ====Control: Variability between samples==== *PGP1f V4 S2 vs PGP1f V4 S5 *Normalize counts with V4 in vitro counts and log transform [[File:PGP1fV4_log_norm_S2_vs_S5.jpeg | 450px]] ====V4 vs V7==== *PGP1f V4 (S2+S5) vs PGP1f V7 (S1) *Log transform [[File:PGP1f_log_sum_V4_vs_V7.jpeg | 450px]] *Normalize counts with in vitro counts and log transform **Low correlation is disheartening, maybe V7 in vitro counts are off [[File:PGP1f_log_norm_V4_vs_V7.jpeg | 450px]] ====PGP1f vs BA8==== *PGP1f V4 (S2+S5) vs BA8 V4 (S1) *Log transform [[File:V4_log_PGP1f_vs_BA8.jpeg | 450px]] *Normalize counts with V4 in vitro counts and log transform **Very high correlation, [[Matt:LabNotes/2015-3-19#DARTFISH_vs_Bulk_Tissue|DARTFISH BA8 correlates better with DARTFISH PGP1f than RNA-Seq BA8]] **Could be the low integer values (many genes with only 1-3 counts) combined with same normalization count in denominator make correlation look better [[File:V4_log_norm_PGP1f_vs_BA8.jpeg | 450px]] ====PGP1f: DARTFISH vs RNA-Seq==== *Data from http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-54733/ **RNA-Seq data cited by FISSEQ paper **File: GSM1322928_results_s_6.txt *Convert RefSeq mRNA ID to HUGO symbol with Biomart **Some genes have multiple RefSeq IDs for one HUGO symbol *Use sum of isoform FPKM values for gene FPKM value *V4 [[File:PGP1fV4_logDARTFISH_vs_logRNASeq_regression.jpeg | 450px]] *V7 [[File:PGP1fV7_logDARTFISH_vs_logRNASeq_regression.jpeg | 450px]] ====PGP1f: DARTFISH vs Illumina BeadArray==== *http://genome-tech.ucsd.edu/public/iPSData/Jay_lee_Jan_2008_Illumina_gene_expression.xls *Used Biomart to convert RefSeq mRNA Acc ID to HGNC symbol **Many did not have an HGNC symbol but these genes were mostly pseudogenes or other anomalies *Created file with only HGNC symbol and gene expression (no headers): Jay_lee_Jan_2008_Illumina_gene_expression.txt **Multiple rows with same gene... ***Take average value: Jay_lee_Jan_2008_Illumina_gene_expression_avgcollapsed.txt ***Take max value: Jay_lee_Jan_2008_Illumina_gene_expression_maxcollapsed.txt =====Using Average===== *V4 [[File:PGP1fV4_logDARTFISH_vs_logBeadArrayAvg_regression.jpeg|450px]] *V7 [[File:PGP1fV7_logDARTFISH_vs_logBeadArrayAvg_regression.jpeg|450px]] =====Using Max===== *V4 [[File:PGP1fV4_logDARTFISH_vs_logBeadArrayMax_regression.jpeg|450px]] *V7 [[File:PGP1fV7_logDARTFISH_vs_logBeadArrayMax_regression.jpeg|450px]] ====PGP1f: DARTFISH vs FISSEQv1==== *V4V7_Genes_CompareJayFISSEQData.xlsx **Counts are from FISSEQ_Science_2014_SeqData_csv\Fibroblast.FISSEQ.2013.06.06.RHex.29bp *V4 [[File:PGP1fV4_logDARTFISH_vs_logFISSEQv1_regression.jpeg|450px]] *V7 [[File:PGP1fV7_logDARTFISH_vs_logFISSEQv1_regression.jpeg|450px]] ====PGP1f: DARTFISH vs FISSEQv2==== *FISSEQvsCellTypeSpecificRNA_Seq.xlsx *V4 [[File:PGP1fV4_logDARTFISH_vs_logFISSEQv2_regression.jpeg |450px]] *V7 [[File:PGP1fV7_logDARTFISH_vs_logFISSEQv2_regression.jpeg |450px]] ====PGP1f: DARTFISH vs RNA-Seqv2==== *FISSEQvsCellTypeSpecificRNA_Seq.xlsx **Has a column labeled "fibro" which I think is RNA-Seq data? Must ask Hosuk where he got it from *V4 [[File:PGP1fV4_logDARTFISH_vs_logRNASeqv2_regression.jpeg|450px]] *V7 [[File:PGP1fV7_logDARTFISH_vs_logRNASeqv2_regression.jpeg|450px]] ====FISSEQv1 vs FISSEQv2==== *Very few data points because only including genes in V4/V7 probeset AND that are present in both FISSEQv1 and FISSEQv2 data sets [[File:PGP1f_FISSEQv1_vs_FISSEQv2_regression.jpeg|450px]]
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information