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Table 3 Analysis steps and the corresponding procedures

From: Tools for T-RFLP data analysis using Excel

Step Macro name Input sheet Output sheet
Prepare the data
1 A_Prepare_Alignment Input Data AppliedPDTandAnalysisRange
TempWorking
InData
TempInData
Normalize replicate profiles
2 Relevant data is copied to InData AppliedPDTandAnalysisRange InData
3 alt. 1 B_Normalize_replicates_TFNAreas InData NormalizedReplicatesAreas
3 alt. 2 B_Normalize_replicates_TFNAreas_LT InData NormalizedReplicatesAreasLT
3 alt. 3 B_Normalize_replicates_TFNHeights InData NormalizedReplicatesHeights
3 alt. 4 B_Normalize_all_FPTAreas InData AllNormalizedFPTAreas
3 alt. 5 B_Normalize_all_FPTHeights InData AllNormalizedFPTHeights
Align replicate profiles
4 Relevant data is copied to InData E.g. NormalizedReplicatesHeights InData
5 C_Align_replicate_profiles InData ReplicateSamplesAligned
Correct the alignment
6 D_FindAndCorrect-AmbiguousAlignments InData CorrectedRepSamplesAligned
Check and correct for systematic differences in size estimation between replicates
7 Relevant data is copied to InData E.g. CorrectedRepSamplesAligned InData
8 D_CheckReplicateSystematicShifts InData RepSystematicShiftCheck
RepSystematicShiftMatrix
9 F_ShiftCorrectedReplicateSizes InData ReplicateRelativeSizes
NewReplicateSizes
NewReplicateSizesAligned
Create consensus profiles
10 Relevant data is copied to InData E.g. CorrectedRepSamplesAligned InData
11 alt. 1 G_RepConsensus_Average InData RepConsensus
11 alt. 2 G_RepConsensus_Sum InData RepConsensusSum
Normalize consensus profiles
12 Relevant data is copied to InData E.g. RepConsensus InData
13 alt. 1 H_Normalize_all_TFNAreas InData AllNormalizedTFNAreas
13 alt. 2 H_Normalize_all_TFNHeights InData AllNormalizedTFNHeights
13 alt. 3 B_Normalize_all_FPTAreas InData AllNormalizedFPTAreas
13 alt. 4 B_Normalize_all_FPTHeights InData AllNormalizedFPTHeights
Align consensus profiles
14 Relevant data is copied to InData E.g. AllNormalizedTFNHeights InData
15 I_Align_consensus_profiles InData AlignedConsensus
16 J_Check_AlignedConsensus AlignedConsensus AlignedConsensus
Check and correct for systematic differences in size estimation between consensus profiles
17 Relevant data is copied to InData E.g. AlignedConsensus InData
18 K_CheckConsensusSystematicShifts InData ConsSystematicShiftCheck
ConsSystematicShiftMatrix
19 L_Shift_corrected_consensus_sizes InData ConsensusRelativeSizes
    ConsRelativeSizesStDevs
    AlignedConsShiftCorrSizes
Calculate the relative abundances of the T-RFs
20 Relevant data is copied to InData E.g. AlignedConsensus InData
21 alt. 1 M_Relative_abundance_Areas InData RelativeAbundanceAreas
21 alt. 2 M_Relative_abundance_Heights InData RelativeAbundanceHeights
Calculate association coefficients
22 Relevant data is copied to InData E.g. RelativeAbundanceHeights InData
23 N_BrayCurtis_matrix InData BrayCurtisMatrix
24 O_JaccardCoeff_matrix InData JaccardCoeffMatrix
Calculate diversity index
25 Relevant data is copied to InData E.g. RelativeAbundanceHeights InData
26 P_ShannonIndex InData Shannon Index