Unable to run tximport using sample.info ?
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Last seen 9 months ago

Thanks for the tximport package, I'm hardcore biologist doing PhD in genomics, it so frustrating for me to use R for data analysis work. That too working with non-model organisms no one had heard of before. After de novo assembly step I used salmon for quantification and generated the quant.sf files for 30 datasets. I used trinity abundance matrix generator scripts to generate gene counts.matrix for all the samples. How do I combine all the matrices into a single matrix which I'll be fed into DESeq2/EdgeR packages. The organism I'm working for doesn't have any information in the public domain. I'm facing an error while loading samples.txt file, saying the matrix is not correct. Please find the sample.info file.

sample  treatment  replicate
9_S5      Model 1
10_S9     Model 2
11_S13    Model 3
12_S17    Model 4
13_S21    Model 5
14_S26    Model 6
15_S30    Model 7
16_S2     Model 8
17_S6     Sal       1
18_S10    Sal       2
19_S14    Sal       3
20_S18    Sal       4
21_S22    Sal       5
22_S27    Sal       6
23_S31    Sal       7
24_S23    Sal       8
25_S28    Control      1
26_S32    Control      2
27_S3     Control      3
28_S7     Control      4
29_S11    Control      5
30_S15    Control      6
31_S19    Control      7
32_S24    Control      8
1_S4      Odor         1
2_S8      Odor         2
3_S12     Odor         3
4_S16     Odor         4
5_S20     Odor         5
6_S25     Odor         6
7_S29     Odor         7
8_S1      Odor         8

Suggestions please.

Thanks Kevin

tximport deseq2 edgeR • 148 views
Entering edit mode
Last seen 6 hours ago
United States

The support site is for specific software questions, if you find an error with a particular package, provide the error, your code and tag the relevant package. Here you've tagged edgeR and DESeq2 which are developed by different maintainers, and then the support site emailed both development teams, yet you haven't provided the error or the code you used. I'd suggest making a new post where you tag the relevant package, and provide the error and the code.


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