Working with Statisticians

Working with Statisticians

At some point, a statistician is likely to be asked to analyze your data. This

can lead to much unhappiness.

STATISTICIANS COME IN MANY SHAPES AND SIZES

BUT

Data formats

• Ideally, use a normalized database with validated data entry as part of LIMS…

• But 99% of the time => Excel spreadsheet• Some statisticians prefer to work with raw

data (i.e. FCS files) but not common– Scott will cover consistent annotation for raw data

at another lecture

Basic principle #1

• Statisticians do not like Excel– The first thing they will try to do is export to a CSV

or delimited file, for import into SAS or R– If this is difficult to do, they will not like you

Excel rules for happy statisticians

• 1 worksheet = 1 table• 1 cell = 1 value• Data?• Metadata?• Formatting?• Validation?

1 worksheet = 1 table

• A table has column headers and a number of rows and nothing else – it is RECTANGULAR

• Do not put more than 1 table in a worksheet• Do not use non-rectangular tables• Example of good worksheet

1 worksheet = 1 table

1 cell = 1 value

• Easy to filter by tube, sample or subject• Easy to write validation rules or lookup table

1 cell = 1 value

• ID column has 3 different values• Need to do text parsing to recover information

– very error prone

Data: column names

• Consistent column names across worksheets– Singlets/Lymphocytes– Singlet/Lymphs– Singlets / Lymphocytes– Singlets/Lymphoctyes

• Use full gating path for column name– Singlets/Lymphocytes/Viable/CD4+/CM/IFN+

Data: What to record • Better to have more data than less data

– Sample type (PBMC, whole blood)– Recovery – Viability

• Better to have basic than derived data– Counts better than relative frequencies

• Keep link to raw data for reproducibility– Path to FCS file on server

• Use special indicator for missing data (e.g. NAN), not zero• Can have extra column for notes

– Ideally codified so Error 23 rather than “Sample sat > 8 hours before processing”

Data: Versioning

• Do not change the data in the worksheet once it has been handed to statistician.

• If there are errors that must be corrected, make a new copy, label the filename with date and version, and send that to statistician– ArcticRatExperiment_07May2013_Version01.xlsx– ArcticRatExperiment_17May2013_Version02.xlsx

Metadata

• Should have SOP document for metadata– How missing data is represented (e.g. NA or blank)– Keys for interpretation – e.g. Table of error codes– Contact person: phone #, email– Metadata can be in 2nd worksheet or separate document

• Gating scheme with labeled gates matching cell subsets used in column names (PDF or PPT)

• Panel information– Antibodies, clones, batches, fluorochromes, peptide mixes

• Path to Flowjo .jo or .xml analysis file

Metadata

• There are minimal information standards that should be followed– MiFlowcyte– MIATA

• Google for them if you’re not familiar with them – increasingly these are required by journals for publication, so worth making it an SOP for documentation of results

Formatting

• Don’t do it.• Avoid putting information via:– Highlighting– Fancy spacing– Different fonts and font effects– Merging cells– Comments

• Will it survive a round-trip from Excel to CSV and back again?

Formatting - Before

Formatting - After

Comments are lostHighlighting is lostBad cell formatting is lostMerged cells become missing information

Validation

• Can set up validation rules in Excel to minimize data entry errors:– Number range (0, 10000000)

• Can use lookup tables for codes to use– E.g. Error codes with explanation

• If possible, once format for data is decided, get local Excel wizard to create template and lookup rules

Questions?

• If no questions and need to kill time, watch Biologist talks to Statistician video– http://www.youtube.com/watch?v=Hz1fyhVOjr4