Wiki » History » Version 2
Katie Lennard, 10/07/2020 04:24 PM
| 1 | 1 | Katie Lennard | # Wiki |
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| 3 | # Data analysis background |
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| 5 | The data was originally analysed by overseas collaborators (Hans mollenkopf@mpiib-berlin.mpg.de and Natalie natalie.nieuwenhuizen@uni-wuerzburg.de). Hans provided .RData objects and .RMD file summarizing his results, which were quite comprehensive (including exploratory analysis, differential expression using limma and gene module enrichment using the R package tmod). However there are very strong batch effects in this dataset that correspond to RNA extraction date in the lab. I therefore redid the analysis with combat batch correction (which was only possible by correcting the astrocyte and neuron samples separately). They were therefore analysed sepearately downstream. |
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| 7 | # Data preprocessing |
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| 8 | Hans performed background correction (normexp method) and normalization (quantile). The data was supplied to me as .RData objects (raw and normalized). I added ComBat batch correction. |
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| 10 | # Downstream analysis (see attached powerpoint) |
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| 12 | PCA, tSNE multivariate |
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| 14 | Differential expression analysis between groups: |
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| 15 | Astrocytes: not infected vs. H37Rv; not infected vs BC; BCG vs H37Rv |
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| 16 | Neurons: not infected vs. H37Rv |
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| 18 | Transcriptional module testing: using R package tmod |
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| 19 | 2 | Katie Lennard | |
| 20 | Signaling Pathway Impact Analysis (SPIA) for neurons (NI vs. RV) and astrocytes (NI vs. RV). |