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