while designing matrix i got an error, please help me out
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Rishav • 0
@rishav-25031
Last seen 4 hours ago
Patna

During performing analysis of my data, I got an error while designing the matrix. please help me out.

Here is the code that I run


#  condition_pairs <- t(combn(levels(HB$Treatment), 2))
Error in combn(levels(HB$Treatment), 2) : n < m

# Here is my metadata named HB

Run                 collection_time                        Sample Name               Treatment
SRR1984269  24h post-plating                            GSM1663548               Uninfected
SRR1984270  48h post-plating                        GSM1663549               Uninfected
SRR1984275  72h post-plating                            GSM1663554                Uninfected
SRR1984276  48h post-plating/24h post-infect    GSM1663555            AdGFP-infected
SRR1984279  48h post-plating/24h post-infect    GSM1663558            AdHBV-infected
SRR1984281  48h post-plating/24h post-infect    GSM1663560            AdHBV-infected
SRR1984285  72h post-plating/48h post-infection GSM1663564             AdHBV-infected
SRR1984271  48h post-plating                             GSM1663550                 Uninfected
SRR1984282  72h post-plating/48h post-infection GSM1663561             AdGFP-infected
SRR1984284  72h post-plating/48h post-infection GSM1663563              AdGFP-infected
SRR1984266  Freshly isolated/unplated           GSM1663545                    Uninfected
SRR1984280  48h post-plating/24h post-infect     GSM1663559           AdHBV-infected
SRR1984265  Freshly isolated/unplated            GSM1663544                  Uninfected
SRR1984267  Freshly isolated/unplated            GSM1663546                  Uninfected
SRR1984268  24h post-plating                             GSM1663547                 Uninfected
SRR1984272  48h post-plating                             GSM1663551                 Uninfected
SRR1984283  72h post-plating/48h post-infection  GSM1663562           AdGFP-infected
SRR1984286  72h post-plating/48h post-infection  GSM1663565            AdHBV-infected
SRR1984287  72h post-plating/48h post-infection  GSM1663566           AdHBV-infected
SRR1984273  72h post-plating                             GSM1663552                  Uninfected
SRR1984274  72h post-plating                             GSM1663553                Uninfected
SRR1984277  48h post-plating/24h post-infect     GSM1663556            AdGFP-infected
SRR1984278  48h post-plating/24h post-infect     GSM1663557             AdGFP-infected
RNASeqR • 143 views
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Can you tell us the output of class(HB$Treatment) ? It should be "factor"

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The output of class HB($Treatment)

[1] "character"

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Try class(HB$Treatment) <- "factor" and combn should work

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you mean the code should be

condition_pairs <- combn(class(HB$Treatment), 2)
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1
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You should precise what is your expected output in your post as it is difficult to help you. If you want to remove the error you could do : condition_pairs <- t(combn(unique(HB$Treatment), 2))

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