Tools for T-RFLP data analysis using Excel

Fredriksson, Nils Johan; Hermansson, Malte; Wilén, Britt-Marie

doi:10.1186/s12859-014-0361-7

BMC Bioinformatics

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
8	D_CheckReplicateSystematicShifts	InData	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
18	K_CheckConsensusSystematicShifts	InData	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

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com